The Hatters had been missing the energetic running of the injured Liam Dickinson until manager Jim Gannon made two inspired substitutions which put the side on top sending on Le Fondre and Harpal Singh to bolster the attack.
Dickinson had been ruled out by injury and County badly missed him as Richard Walker put the home side ahead shortly before half time.
It came from a corner and brought goalkeeper James Spencer a yellow card for arguing the ball had not crossed the line.
Earlier there had been a lengthy hold up while Spencer received treatment for a facial injury but when he recovered he kept his side in the game.
Gannon made the first of his changes at half time sending on his latest signing Newcastle's Daryl Smylie for the second half in place of Keith Briggs.
But the game appeared to be going all Rovers' way when they were given a penalty early in the second half for handball against Ashley Williams.
It was a harsh decision for Williams was on the by line and away from goal but Walker stepped up to hit his 16th goal this season wide of Spencer's left hand.
But with Smylie taking control of the midfield and the other two subs running hard Rovers were very much on the back foot.
Le Fondre's first goal came as he ran onto a long through ball from Smylie to beat a keeper who had stayed on his line.
Rovers looked to have been denied a second penalty right near the end when Mark Hughes seemed to handle on the goal line.
County made the most of their luck as Le Fondre went away near the end to beat Scott Shearer with a diving header, although defenders claimed he met the ball with his fist.