The Mariners took the lead through Oumare Tounkara on 16 minutes and they could have doubled it on the half-hour but Scott Neilson saw his penalty saved after Tounkara was fouled inside the box.
Struggling Chester came into the game more in the second half but Town made the points safe when substitute Andy Cook struck with six minutes to go.
Substitute James Caton pulled one back for the visitors in stoppage time when his cross looped into the net at the far post for 2-1.
But Grimsby survived their late scare to collect all three points and stay third in the Skrill Premier table.
After changing his entire outfield line-up for the game at Dartford on Thursday, Town boss Paul Hurst reverted to a more familiar starting XI.
Instead, there were two changes from the side that secured a dramatic late draw against Woking on Tuesday, with Paddy McLaughlin coming in for the injured Aswad Thomas and suspended Jamal Fyfield at left-back.
Tounkara, who did play at Dartford along with McLaughlin and keeper James McKeown, was the other to stay in the team, although Lenell John-Lewis had been named on the original teamsheet before picking up an injury in the pre-match warm-up.
McKeown started in goal, with Sam Hatton, Shaun Pearson, Andrew Boyce and McLaughlin forming the defence.
Alex Rodman, Craig Disley, Scott Kerr and Scott Neilson were the midfielders, with Tounkara and Connor Jennings named as the attackers.
The Grimsby subs were Clayton McDonald, Ross Hannah, Andi Thanoj, Caine Winfarrah and Cook.
Chester made the journey east looking for a victory that would help their fight against relegation.
The Blues side included striker John Rooney, brother of Manchester United star Wayne, while former Town defender Paul Linwood was named on the visitors’ bench.
The game kicked off seven minutes later than usual to commemorate the 25th anniversary of the Hillsborough disaster, with supporters impeccably observing a minute’s silence at 3.06pm.
An early run from Rodman led to a throw-in on the right, which was claimed by keeper Aaron Chapman.
Kerr hit a shot over the bar on four minutes as Town started brightly, although neither keeper had been called into action at the end of the first 10 minutes.
A foul on Craig Hobson gave Chester a free kick near the halfway line but Rooney’s delivery into the penalty area was headed clear by Boyce.
A forward run down the middle from Neilson looked to have provided a spark, although his 20-yard shot was pushed out by Chapman.
Town retained possession though and when the ball was worked back through Rodman, he pulled the ball back and TOUNKARA was there top finish from 15 yards, finding the bottom corner of the net.
The visitors thought they had equalised within two minutes when the ball was in the net at the other end but the offside flag had gone up, meaning Grimsby’s lead remained intact.
Lewis Turner was brought down by McLaughlin to the right of the Town box and after the Irishman escaped a yellow card, Rooney’s free kick was headed away by Disley after Chester’s Michael Kay had won the initial header.
Neilson tried a first-time shot from 25 yards that landed on the roof of the Osmond Stand on 26 minutes, with the hosts still looking the better of the two sides and doing most of the attacking.
At the other end, a cross from Turner came in after Andy Bond had sent him away down the right but after the winger failed to pick out a team-mate, Disley calmly headed back to McKeown.
Town were given a golden chance to double their advantage when Tounkara was fouled inside the box on the half-hour and referee Richard Wigglesworth pointed to the spot.
After a discussion between several Grimsby players as to who would take the penalty, Neilson eventually stepped up but his shot was comfortably saved by keeper Chapman, who guessed correctly and dived to his right to push the ball away.
A brief delay came when Chapman needed treatment after a challenge with Tounkara but the keeper was passed fit to play on.
Neilson looked to make amends for the penalty miss when he won the ball in midfield and did well to turn away from his marker but after advancing down the middle, the winger’s through-ball was much too strong for Jennings to catch.
A Town free kick from the right was whipped in by McLaughlin six minutes before the break but defender Luke Ashworth got to the ball ahead of Pearson to head clear.
Another Rooney free kick was dealt with by the home defence, before a foul by Rodman gave Kevin McIntyre an opportunity to get the ball into the box again, although this time, the delivery was cleared by Boyce.
Two added minutes were played at the end of the half and a Rooney shot from 20 yards was blocked for Chester as the visitors looked to get back into the game before the interval.
They were unable to do so though, with the referee’s half-time whistle meaning Grimsby went into the dressing rooms with the advantage.
James Caton replaced Turner for the visitors before the restart and the first chance of the second half went to the Mariners a minute in, when Rodman had a shot blocked after a jinking run from Neilson.
Hobson was shown the first yellow card for a foul 25 yards from the Town goal, before Jennings controlled a long through-ball from Hatton and won a corner on the right, which led to a shot from Neilson being blocked.
Substitute Caton cut in from the Chester right and hit a shot that flew over the bar on 53 minutes, with McKeown still not called into any serious action by the visiting attack.
A low cross from Craig Mahon was dealt with by Pearson as Chester enjoyed a good spell of possession.
The away side’s second substitution saw Danny Carlton replace Hobson as the game entered a scrappy phase.
Town began to show brighter signs when Neilson found Jennings on the edge of the box but he was outmuscled by a defender.
Jennings was then brought down as the Mariners launched their next attack but McLaughlin’s free kick from 30 yards was chipped into the box and nobody got a touch as it went out for a goal kick.
Tounkara beat his man to create a shooting chance for himself soon afterwards but his effort lacked power and Chapman gathered the ball.
McLaughlin was booked for a foul on Caton on the Chester right, before Gareth Seddon came on for Bond as manager Steve Burr made his final change.
The free kick was headed out for a corner and after Rooney’s delivery was punched by McKeown to Jason Jarrett at the far post, he could only volley over the bar.
Town had a chance soon afterwards when Neilson found Jennings on the edge of the box but the Scunthorpe loanee sliced his shot wide.
Jarrett fouled Tounkara in midfield after the striker had done well to win the ball back. It proved to be the goalscorer’s last contribution as he was replaced by Cook before the free kick, with just short of 20 minutes left to play.
Town were almost in trouble when a clearance by McLaughlin was charged down and Chester broke. A low cross from the right looked to have caused problems when Pearson stuck a boot out to connect with the ball but luckily for the hosts, it went straight to McKeown.
Cook showed good strength to work an opening on the edge of the box on 75 minutes but he appeared to be off-balance as he dragged his shot wide.
Hatton conceded a corner a minute later but Rooney’s kick was headed away by Disley. The Chester pressure continued with a throw-in, before Town eventually cleared their lines and the pressure was eased when Jennings was fouled, with Jarrett picking up a yellow card.
Kerr almost let the visitors in when he lost possession 25 yards out and Rooney tried a shot that was saved by McKeown, with Seddon unable to profit from the rebound.
Thanoj came on for the last 10 minutes in place of Jennings, who had enjoyed perhaps the best game of his loan spell at Blundell Park so far.
Cook won a corner soon afterwards but it did not lead to a chance in front of goal.
The striker was involved again moments later, taking the ball from Neilson but hitting a weak shot that was comfortable for Chapman in the Chester goal.
Town had come under pressure from their visitors for some of the second half but they made sure of their victory with six minutes to go. Good play by Neilson saw him get to the by-line and cut in before pulling the ball back across the six-yard line for COOK to tap in at the far post.
Cook was booked for a foul just inside the Chester half, before a shot from the visitors went high and wide as the game moved into four minutes of added time.
There was to be a late scare for the hosts when a cross from CATON on the left looped over McKeown and into the net to make it 2-1 with two of the added minutes still to play.
But the hosts were able to hold on and see the game out to collect maximum points and keep their promotion aspirations on track.
Town are next in action on Tuesday, when fellow play-off contenders FC Halifax Town are the visitors to Blundell Park.