Substitute Andy Cook was the hero for the Mariners, scoring two late goals to secure all three points.
In a game lacking in quality from both sides, it took the introduction of Cook and fellow sub Andi Thanoj just before the hour to send the momentum the way of the home side.
Hyde had possibly edged the first half but faded towards the end of the contest and after Cook struck six minutes from time, the relief was evident around the home sections of the ground.
The visitors looked to get themselves back on level terms but Cook’s second in added time made sure of an important Grimsby victory.
Town were forced to make two changes to the side that beat Welling to advance to the quarter-finals of the FA Trophy.
Greg Fleming made his first league start in goal after regular keeper James McKeown was sent home ill before the game, while Joe Colbeck came into the XI in place of Marcus Marshall, who was recalled by parent club Bury.
Fleming started behind an unchanged defensive unit of Sam Hatton, Shaun Pearson, Ian Miller and Bradley Wood, while Colbeck lined up on the right of a midfield that also included Craig Disley, Derek Niven and Jamie Devitt.
Richard Brodie was given the nod to start alongside Ross Hannah in attack, while the Grimsby substitutes were Frankie Artus, Cook, Simon Ford, Dayle Southwell and Thanoj.
Hyde travelled east looking to become the first team to complete a league double over the Mariners this season.
Town were beaten 3-2 in the reverse fixture in Greater Manchester, a result which remains their only defeat on the road so far this campaign.
Hyde named former Grimsby striker Phil Jevons in their starting XI, with the ex-Blundell Park favourite aiming to dent the table-topping ambitions of his former employers.
Town kicked off playing into a strong wind and they won the first corner of the evening through Colbeck on the right two minutes in. The winger took the kick himself but Devitt missed his kick after a low ball was played to him on the edge of the box.
Hyde broke but a good block tackle by Hatton won the ball back and Brodie eventually put a cross-shot out of play for a goal kick.
A free kick to the visitors provided an opportunity to get the ball into the danger zone but winger David Poole could only float it into Fleming’s arms.
A chance for the away side came when Disley gave the ball away to Jevons on the edge of the box on nine minutes. The striker’s cross was headed away by Wood but it was sent back in and headed on by Scott Spencer, although Fleming claimed a comfortable catch.
A foul by Pearson then gave Hyde a free kick in a central position, 25 yards out. Jevons shot but Fleming claimed the ball at the second attempt.
Town were guilty of giving the ball away to often in the early stages but they were given an opening when a foul on Devitt brought a free kick midway inside the Hyde half. The ball was worked to Colbeck on the right but his cross went out of play before it could reach visiting keeper David Carnell.
Good work by Brodie after another free kick led to Niven trying his luck from 25 yards but the midfielder’s wild effort flew over the bar.
Disley was penalised for a foul inside his own half on 22 minutes but midfielder Chris Sedgwick was caught offside from the resulting free kick.
Town had struggled to create anything in the first quarter of the game and that continued when an attempted cross from Brodie on the left was sliced out for a goal kick.
Colbeck had more success with a cross from the opposite flank soon afterwards but Carnell came off his line to collect the ball.
A foul on Devitt earned Hyde midfielder Mark Allott the first booking of the game and the resulting free kick from the right eventually saw the ball find its way to Disley but he could only shoot wide from 15 yards.
Then away side won a corner on the left on 35 minutes but Fleming got a fist to the ball to clear the danger.
The game so far had been scrappy, with Town unable to put their stamp on proceedings and their visitors perhaps the better of the two teams, although a lack of quality was noticeable.
The first moment of quality from the Mariners came on 37 minutes, when a low, cross-field pass from Devitt sent Brodie through but instead of shooting, the Crawley loanee looked to find strike partner Hannah and the ball was cut out.
Hannah had the next opportunity after he was put through down the left but after cutting into the box, he was forced wide and could not trouble Carnell as he shot wide of the near post.
Devitt picked up a loose ball on the edge of the penalty area and had a shot blocked as Town looked to up the tempo with half-time approaching.
One added minute was played at the end of the half and with neither side able to carve out any further chances, the scoreline remained level at the interval.
No changes were made before the restart and Hyde keeper Carnell went down injured within a minute under a challenge from Hannah, who was chasing the ball down. The Town striker was booked for the foul and there was a delay while Carnell received treatment, before being passed fit to continue.
Disley and Colbeck linked up well down the right on 52 minutes for the skipper to get to the byline and send a cross in but Carnell claimed the ball at his near post.
At the other end, a left-wing cross from Adam Griffin looked to cause problems but Spencer and Chris Sedgwick seemed to get in each other’s way in the middle and neither was able to get a good connection on the ball.
Town won a corner on the left on 57 minutes but Colbeck knocked his low delivery out of play at the near post.
The Mariners had posed very little attacking threat so far and the managers’ patience ran out just before the hour, when they sent Cook and Thanoj on for Brodie and Niven.
Thanoj’s first involvement was to play a ball through for Hannah but the striker could not keep his 20-yard shot down, firing the ball over the bar.
Town’s best move of the game came when Devitt played a superb cross-field pass for Colbeck on the edge of the box and he controlled it well before hitting a shot that Carnell had to beat away fir a corner at his near post.
Jevons went down injured in the centre circle on 64 minutes and had to be replaced by Matt Blinkhorn.
A spell of Hyde possession came to nothing as Griffin’s cross from the left was caught by Fleming, with both teams still looking for a breakthrough goal and only 20 minutes left to play.
A deep cross from Wood was headed out for a corner before it could be met by Cook and after Colbeck’s delivery from the flag was half-cleared, Cook hooked a shot over the bar from 20 yards.
Another corner, this time on the opposite side, was not fully dealt with by the Hyde defence but referee Ross Joyce spotted an infringement and blew for a free kick to the visitors.
Hatton smashed a long-range shot well over the bar as Town kept looking for an opening goal.
They went closer on 75 minutes, when a good ball from Wood sent Devitt away down the left. He cut into the box and played a low ball across the six-yard line but Disley could only flick it over the bar.
The Mariners were now looking to play more balls to feet,, with Devitt and Thanoj pulling the strings.
Hannah thought he was through on goal after collecting a pass from Devitt but the offside flag went up against the former Bradford striker.
Devitt then tried to curl a shot towards the far corner of the net after creating an opening on the left but the effort lacked accuracy and drifted high and wide.
Devitt was yellow-carded fir a trip on winger Liam Tomsett, before Southwell replaced Hannah in the Town attack for the last eight minutes of the game.
Southwell almost had an immediate chance when Cook hooked a ball across goal but the ball was too strong for everybody.
Seconds later though, then Mariners had their breakthrough, when a chipped cross from Devitt on the left was met by the head of COOK, who beat keeper Carnell to the ball and nodded it into the net.
Hyde’s response to going behind was good and they won a corner on the right with three minutes to go.
Fleming pushed the ball clear from the flag-kick, before a shot from substitute Ray Putterill was blocked.
Right-back Josh Brizell was replaced by Matt Harris for Hyde as the match moved into four minutes of added time.
Thanoj hit a shot straight at Carnell after a good break by Southwell, with Town looking to hold onto their lead.
And in the end, the Mariners went one better than that, as COOK crafted an opening for himself, before steering a shot beyond Carnell and into the bottom corner of the net with seconds left to play
That put the result beyond doubt and ensured Grimsby regained top spot in the league table, ahead of Saturday’s trip to Cambridge United.