Jamie Vardy's stunning effort saw off Grimsby and extended Fleetwood's unbeaten league run to 21 games.
A Liam Hearn shot, that was deflected in by Fleetwood midfielder Peter Cavanagh, gave Grimsby the lead.
The Cod Army's Richard Brodie had an effort cleared off the line, but Andy Mangan made it 1-1 from the spot after Anthony Church felled Vardy.
Vardy secured the victory late on with a superb effort that flew into the top-right corner.
VIEWS FROM THE DRESSING ROOM
Grimsby Town joint-manager Paul Hurst told BBC Radio Humberside:
"I never really thought it was a penalty, I never had that feeling and the referee certainly delayed his decision and then to top it off apparently a few of their lads have said that it was never a penalty.
"When you hear that it's a difficult one to take.
"For me, the delay in the referee's decision made it clear that it wasn't a penalty and ultimately if that's the case he has to give a corner or a goal kick."
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