It looked like being a frustrating day for the home side against Neil Warnock's Leeds United who saw Zac Thompson red carderd after only 13 minutes.
But Royals struggled to make their numerical advantage count until the closing stages of a firey clash at Madejski Stadium.
Le Fondre eventually broke the deadlock in the 84th minute when he netted from close range after Hal Robson-Kanu had headed Jimmy Kebe's cross back across goal.
And the diminutive striker grabbed his and Reading's second in the 89th minute when he turned in a Jason Roberts shot from a couple of yards out.
The win sent Reading to the top of the Championship table for the first time in six years.
But they could be overtaken again tommorow if Southampton beat Portsmouth.
Royals return to Championship action on Tuesday when they go to Brighton & Hove Albion (7.45pm ko).