Le Fondre struck twice at the Broadfield Stadium as Reading recovered from conceding a goal after just 14 seconds to end Crawley's dreams of another cup adventure.
The npower League One side reached the fifth round in each of the last two seasons and they made the perfect start with a 25-yard strike from the impressive Nicky Adams.
At that point Le Fondre feared the worst. Reading, with just one victory from 10 matches, could have panicked at the prospect of being the victim of an FA Cup upset.
But they did not. Le Fondre drew Reading level and then sealed the victory from the penalty spot after strike partner Noel Hunt had put the Royals ahead.
The challenge now is to take that composure and the momentum of two wins from three matches - following their home victory over West Ham - into next weekend's Premier League clash with West Brom.
"It gives everyone a boost. It builds us a little bit of momentum towards next week when we've got West Brom at home," Le Fondre said.
"We want to get momentum and take it on to our Premier League form.
"I think we can build on this as a team. It gives us a lot of confidence as a squad and a lot of momentum going into the West Brom and Newcastle games.
"A few players were rested but we've come in and done a job. That's what the main thing is for the whole squad - we're in it together and will take this on to the Premier League.
"Crawley made it hard for us but we regained our calmness (after they scored). That was the main thing.
"We've shown great character in all the games we've played in and this was no different.
"We stuck to our game plan, got the ball wide, got our wingers on it, got the ball in the box and me and Hunty took care of that really."
Crawley manager Richie Barker was envious at the striking talent available to Reading, who brought both Le Fondre and Hunt into the starting line-up after a busy Christmas schedule.
But Barker is also realistic. He fears players like Adams could be snapped up in the January transfer window and he took a pop at the expectations held by some of the club's supporters.
After Reading had taken control of the game, a section of the fans at one end began to chant at Barker to 'sort it out'.
Barker said: "You can't educate some people, can you? I will do the best I can and one day when I've gone, a bit like my old club (Bury), people will realise how well I did.
"The expectations (among some supporters) are ridiculous.
"We have given a Premiership team a real good go. We created enough chances to be ahead but their goalkeeper pulled off two or three really good saves.
"To put their goalkeeper under as much pressure as we did, for a League One team against a Premier League side, speaks volumes about the players.
"I thought we would create something every time we went forward. Their quality in the final third defined the fact we were a goal down at half-time. Adam Le Fondre and Hunt are good players."
Reading manager Brian McDermott, who has the support of his side's fans despite their struggles at the bottom of the Premier League, backed Barker.
"Sometimes you have to remember where you have come from and in a short space of time how well Crawley have done," McDermott said.