Le Fondre's double strike was just reward for the Royals, who had commanded possession and territory for much of the match, only to find themselves twice having to come from behind.
After a goalless first half, Theo Robinson opened the scoring for Derby on 59 minutes with a back-post tap-in before Le Fondre's superb volley levelled matters six minutes later.
Tomasz Cywka regained the lead for the visitors on 75 minutes, sliding in to push the ball past Adam Federici in the Reading goal, but Le Fondre headed in Hal Robson-Kanu's centre to tie the game once more.
Derby barely put together a notable run of play throughout the 90 minutes, and were lucky to return to Pride Park with a share of the spoils. The Rams have now failed to win in their past four npower Championship outings.
Reading wasted a glorious opening five minutes into the match when Mikele Leigertwood steamed from his own half to the edge of the Derby penalty area.
Leigertwood had the opportunity to slip in Jimmy Kebe, who was in plenty of space inside the box, but instead went for glory and stubbed a woeful effort wide of Frank Fielding's right-hand post.
Moments later, Joseph Mills had another gilt-edged chance to open the scoring, but the full-back's tame left-footed shot was little cause for alarm for the Derby stopper.
Leigertwood fired over the crossbar from distance on 20 minutes, Kebe saw his side-footed attempt from 15 yards blocked en route to the bottom corner eight minutes later and Le Fondre guided a gentle long-range curler into Fielding's arms.
Fielding did brilliantly to get down low to his left to stop Le Fondre's accurate header from Mills' free-kick, and it took until the 32nd minute for Derby to have a shot on target - Federici comfortably gathering Jamie Ward's eight-yard back-heel.
After the teams went into the break goalless Reading started the second period in the manner they had finished the first.
But while Derby at least had a speculative Ward drive from range to show for their meagre endeavour in the final third, the Royals could not muster a shot of any kind.
And that profligacy up front was punished by the visitors on 59 minutes when Ben Davies whipped in a free-kick from the right and Robinson was on hand at the back post to slot beneath Federici.
The tide seemed to be turning towards the visitors for the first time, but Reading soon stemmed the flow and were level on 65 minutes.
Jem Karacan nodded Mills' looping cross towards the former Rotherham striker and Le Fondre obliged with a over Fielding and into the back of the net.
But with their second shot on target, Derby pushed in front once again.
Davies provided the centre and Cywka wrestled off the attention of Mills at the back post to bundle the ball past Federici on 75 minutes.
This time, however, the lead lasted just two minutes.
Hal Robson-Kanu took the ball on the left wing and produced a sweet, fizzing cross right onto the forehead of Le Fondre, who nodded confidently beyond Fielding.