Dean Gordon's late winner earned Grimsby only their second away success in ten months as the Mariners ended Northampton's recent good run.
And the Cobblers could have few complaints about the result after failing to produce enough in the final third to test Grimsby keeper Tony Williams.
Gordon's 87th minute winner gave Northampton little time to salvage a point from the contest.
Northampton started brightly enough and when Eric Sabin burst into the box early on, he forced Williams to make a fine save at his near post, before heading weakly at the Grimsby keeper.
Grimsby had their moments with Colin Cramb forcing Paul Rachubka to make a smart save while Gordon was off-target with one long-range effort before finding the side-netting with a free-kick.
Michael Reddy forced Rachbaka to save his header while Andy Parkinson was just off target from the edge of the box.
Chris Willmott headed just over for Northampton just after the break while Tommy Jaszczun saw his shot blocked from a corner before Grimsby substitute Ashley Sestanovich struck the bar with his 73rd minute drive.
But with three minutes remaining Gordon got on the end of Thomas Pinault's free-kick and his header flew in off the underside of the bar despite Rachbaka getting a hand to the ball.
Martin Smith, who had earlier gone close with a free-kick, almost salvaged a point for the hosts, but his late header flashed just the wrong side of the upright.