Le Fondre set his side on their way to a comprehensive victory with three goals in the opening 33 minutes, two from close range and one from a precise finish after good work by Pavel Pogrebnyak.
The big Russian striker then added a fourth from the penalty spot just before the break as Reading all but had the points sewn up by the interval.
The home side then piled on the agony after the break with further goals from Kaspars Gorkss, Hope Akpan and Nick Blackman before sorry Bolton pulled a late goal back through David Ngog, although it was of little consolation for the visitors.
Reading went into the match with only one win in their last six matches and with an array of key players absent due to injury.
Bolton, meanwhile, had suffered only one defeat in six games and were unbeaten in three, with Dougie Freeman's team having shown steady improvement since being bottom of the division in late September.
That form would have given Bolton hope heading into the clash but they soon found themselves on the back foot as Reading started well.
Le Fondre shot wide early on after getting on the end of a Chris Gunter cross but his name was soon on the scoresheet as he opened the scoring in the 12th minute.
Garath McCleary cut in from the left wing and although he tumbled to the floor and lost possession, Le Fondre was in the right place to thunder in the loose ball for his eighth goal of the season.
Bolton should have equalised soon after an error by Reading defender Alex Pearce allowed Ngog to go through on goal, but he was foiled by a sprawling save from keeper Alex McCarthy.
Bolton would pay for the miss, with Le Fondre scoring twice in five minutes to complete his treble and establish a 3-0 lead.
First, he ran on to Pogrebnyak's clever headed flick to coolly beat Bolton keeper Andy Lonergan, and then he tapped home from close range after McCleary had unselfishly passed to him following a mistake by Tim Ream.
That treble took just 21 minutes, and just before half-time Reading increased their advantage when Alex Baptiste carelessly handled an attempted Jordan Obita centre and Pogrebnyak slotted in the penalty past Lonergan.
With the contest effectively over, Bolton set about restoring some pride in the second half.
On the hour, though, Reading scored their fifth.
Pearce's miscued shot was returned into the area by McCleary and centre-back Gorkss stabbed in his second goal in as many games.
Akpan compounded Bolton's misery in the 74th minute when he lashed the ball high into the net from close range and then, four minutes later, substitute Blackman's fierce shot looped in via a deflection off Zat Knight to make it 7-0.
Ngog grabbed a goal back from Bolton near the end after a goalmouth scramble but the contest was already well over by then as Reading climbed back into the top six above Brighton.