Forced onto the back foot for most of the game the Mariners spurned the games outstanding chances with 15 minutes left when midfielder Ciaran Toner fired wide with the goal at his mercy after being set up by substitute Gary Jones.
Northampton also came on strong late in the game and that was due in small part to the arrival of Andy Kirk, the striker who has been out injured since August.
Within minutes of his arrival, Kirk had delivered a dangerous cross which Scott McGleish directed just over the bar and with three potential goal grabbers on the field for the finale, Kirk's sharp turn and shot from the edge of the box in injury time grazed a Grimsby post.
The first half had seen Northampton dominate, but fail to break down a rugged visitors back line well marshalled by skipper Justin Whittle and Robert Jones. After just 27 seconds Martin Smith tested Steve Mildenhall in the visitors goal while in a lively opening, a cross by Junior Mendes was met at near post by Josh Low only for Mildenhall to make an instinctive save.
Quick thinking by Smith in the 16th minute almost broke the deadlock after the Mariners were guilty of a sloppy clearance but with Mildenhall out of his goal, Smith's shot just evaded the far post.
The home side were forced into a defensive reshuffle in the 27th minute when skipper Sean Dyche hobbled from the field with a calf injury but they still carried the greater threat and a Mendes cross forced Whittle into a diving header which just cleared his own cross bar.