The visitors to the Madejski Stadium wilted in the late stages after losing captain Rob Jones to injury, and having already used their allocation of substitutes they were left exposed, allowing Reading to stretch their narrow 2-1 lead to the final comfortable margin of victory.
Reading went ahead early on when midfielder Danny Guthrie guided a long-range shot high into the roof of the net, but Doncaster levelled when substitute Theo Robinson latched on to a loose ball in the home area.
Reading regained their lead through Le Fondre before half-time and added two goals in the second half through Garath McCleary and Pavel Pogrebnyak.
Reading's unbeaten six-match run had ended in their previous outing, a 2-1 defeat at Burnley, but they appeared eager to make amends early on, dominating Doncaster with a series of slick moves.
Jordan Obita miscued a close-range shot, from a McCleary cross, and the 19-year-old winger also blazed over another attempt from 20 yards.
Doncaster were hanging on grimly but were only able to hold out until the 11th minute, when Reading went ahead after excellent approach work by Le Fondre and Pogrebnyak.
The Russian striker chipped the ball to McCleary, whose instant pass was fired high into the net by Guthrie for his third goal in four matches and fourth of the season.
Helpless Doncaster goalkeeper Ross Turnbull had little chance of saving the well-struck effort but did better soon after, when clawing the ball back off the goalline - before it had crossed - after Obita had directed Le Fondre's knockdown goalwards.
Pogrebnyak nodded over and Turnbull saved well from another Guthrie snapshot as Reading kept up the pressure.
Doncaster manager Paul Dickov had seen enough and brought on striker Robinson to replace midfielder Dean Furman after 23 minutes.
Eight minutes later, the move paid dividends when Robinson lashed in the rebound after Reading goalkeeper Adam Federici had spectacularly saved Mark Duffy's free-kick.
Revitalised Doncaster could even have gone ahead when centre-back Bongani Khumalo rose alone at the far post to meet a Duffy corner but the former Reading loanee nodded wastefully over.
Relieved Reading replied by retaking the lead six minutes before the break when Le Fondre cleverly flicked in McCleary's pass.
Robinson continued to make his presence felt and, in the early stages of the second half, twice attempted to test Federici, who was making his first league appearance of the season due to regular goalkeeper Alex McCarthy suffering a knee injury in training.
Robinson's first effort flew over and Federici comfortably saved his second.
Reading replied when Le Fondre headed wide, from a Chris Gunter cross, but only made their pressure tell when Doncaster were reduced to 10 men with 12 minutes left.
Jones had to leave the pitch with an arm injury, meaning Dickov had to make do with 10 men, and McCleary slotted home after good work by Hal Robson-Kanu.
Pogrebnyak scored Reading's fourth from close range deep into stoppage time to seal victory.