Gary Jones scored the only goal as Town took control of their play-off tie after the first leg victory at Sincil Bank.
And Town claimed a place in the League Two play-off final with a hard-fought 3-1 aggregate win over The Imps.
The Mariners led 1-0 from the first leg at Sincil Bank but City the tie when Marvin Robinson headed home Scott Kerr's first-half free-kick.
However, Ben Futcher's flicked finish put Town back in front and Gary Jones sealed their victory with a header before he was sent off late on.
Grimsby Town: Mildenhall, Croft, Whittle, Robert Jones (Futcher 28), Newey, Cohen (Reddy 59), Bolland, Woodhouse, Parkinson, Gary Jones, Mendes (Toner 76).
Subs Not Used: Goodfellow, Kamudimba.
Sent Off: Gary Jones (90).
Booked: Croft, Whittle.
Goals: Futcher 60, Gary Jones 82.
Lincoln City: Marriott, McAuley, Morgan, McCombe (Mayo 86), Beevers (Green 74), Kerr (Frecklington 77), Brown, Hughes, Forrester, Marvin Robinson, Yeo.
Subs Not Used: Birch, Cryan.
Booked: McCombe, Hughes, Yeo, Frecklington, Green.
Goals: Marvin Robinson 27.
Ref: Mike Dean (Wirral).