Crawley had reached the fifth round in each of the last two seasons and they made the perfect start at the Broadfield Stadium with Nicky Adams' 25-yard strike.
But Le Fondre and then Noel Hunt secured a half-time lead for Reading and they wrapped up the victory 10 minutes after the interval when Le Fondre rammed home his second goal from the penalty spot.
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.
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.
Reading then 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.