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."