The Fiat Yamaha rider has spent part of the past two weeks in a wheelchair having suffered a chipped bone in his left ankle and ligament damage in his right after coming off his bike in practice in Shanghai.
Despite this, however, the Spaniard came in 0.260 seconds behind practice leader Dani Pedrosa while also suffering yet another accident at the end of the closing session.
Lorenzo had finished runner-up to Pedrosa in today's opening session, but fell behind in the second when he came off his bike at the exit of turn one and had to be stretchered off the course.
He will still compete in Sunday's Grand Prix, however, and said that he felt better than in China where he also managed to finish the GP in fourth.
"Physically I feel absolutely fine," he said. "On a circuit like this with so much braking the arms are just as important as the legs.
"I'm better than in China and the injury's healing well. But according to Doctor Mir I won't be fully recovered until the race at Montmelo (on June 8).
"We know the risk we're taking, both me and the doctor, but I want to keep competing and not miss a single race."
Despite the setbacks Lorenzo came in close to the top trio, which along with Pedrosa was rounded off by reigning world champion Casey Stoner in second place (+0.049secs) and Colin Edwards (+0.060secs) of Tech 3 Yamaha in third.
Last year's Le Mans winner, Chris Vermeulen, proved he can be fast in France without the help of the rain by posting the fifth fastest time for Rizla Suzuki, while Valentino Rossi came in sixth after finishing third in the morning but becoming the only rider to lap slower in the afternoon session.