Michael Reddy gave the visitors a 48th minute lead at Edgeley Park as the Hatters struggled to make home advantage pay.
But second-half substitute Le Fondre, who has spent most of the season on the bench, struck with two goals in seven minutes to secure some welcome points.
With Mickael Wolski back in the midfield and Tes Bramble replacing Jermaine Easter - who has been allowed to talk to potential new clubs - County turned in an encouraging first-half performance.
Adam Griffin, last week's loan capture from Oldham, blasted a shot narrowly over after four minutes, but soon after there was a scare from the Mariners when Gary Cohen headed against a County post.
Bramble looked determined to make the most of his chance to shine, and after he was hauled down on the edge of the box on 17 minutes, skipper Matt Hamshaw saw his curling free-kick expertly tipped round the post by Grimsby keeper Steve Mildenhall.
Reddy fired over a rebound after James Spencer had superbly kept out Cohen's drive, but two minutes after the break the Irish striker made no mistake when he fired home sweetly after wrong-footing youngster Michael Raynes.
County kept battling away, however, and Ashley Williams headed just over before Bramble somehow missed an open goal.
It was in the process of that miss that Bramble went down injured, to be replaced by Le Fondre and the 19-year-old it was who really made his mark with two class finishes on 72 and 79 minutes.