League One side Crawley enjoyed a dream start when taking the lead inside the first minute through Nicky Adams, but Le Fondre equalised for Reading on 13 minutes.
The Premier League strugglers edged ahead a minute before half-time through Noel Hunt and Le Fondre made certain of his team's progression with the third goal early in the second half.
After a busy Christmas programme, Reading manager Brian McDermott made seven changes and for 44 minutes it looked like a gamble he might lose as Crawley, buoyed by the early lead, looked more hungry, more organised and they exploited the visitors' vulnerable defence without being able to add to Adams' stunning opener.
Supporters were still taking their seats when Ian Harte, captaining Reading for the first time, was robbed of possession by Adams, who cut in from the right and beat goalkeeper Adam Federici with a 25-yard strike into the top corner.
Billy Clarke saw his shot headed clear by defender Alex Pearce after working space in the Reading box and Adams tried another long-range effort, which this time flew wide.
Federici produced an acrobatic save from Joe Walsh's header before Reading, having weathered a storm for the opening 13 minutes, capitalised from their first real period of pressure.
After a succession of corners, Garath McCleary stooped to meet Harte's cross with a cushioned header back to Le Fondre, who directed a first-time shot low past Crawley goalkeeper Paul Jones.
Crawley continued to ask questions of the flimsy Reading defence, with Federici pressed into action to deny Simpson after another Harte mistake and then Clarke from close range.
But Reading snatched the half-time lead. McCleary's pace and trickery as he ran into the box left Crawley full-back David Hunt on his backside and Hunt turned the cross past Jones.
Reading looked far more composed when they emerged for the second half, with Jem Karacan glancing a header wide before Hunt went down under a challenge from Walsh. Referee Anthony Taylor awarded the penalty, despite the Crawley protestations, and Le Fondre drilled his shot into the roof of the net.
The match was effectively over as a contest at that point as Reading's superior quality began to tell and they bossed the second half, although Le Fondre could not fashion a hat-trick.