Despite Andrea Dovizioso of Repsol Honda going quickest in second practice, the session was affected by rain and so Simoncelli's morning time of one minute 48.987 seconds was the fastest of the day.
Dovizioso, 25, was third quickest in the morning session behind Simoncelli and his team-mate Casey Stoner, although only one tenth of a second split the fastest three riders.
Yamaha Factory Racing duo Jorge Lorenzo and Ben Spies finished fourth and fifth with Colin Edwards sixth, just ahead of the returning Dani Pedrosa, who is back after missing the last three rounds with a fractured collarbone.
The Spaniard has happy memories of Mugello as he led from start to finish in last year's race.
Pedrosa and Championship leader Stoner did not take part in the second session as constant drizzle left a slippery track that was not wet enough for rain tyres.
Most of the field wrote the afternoon off but the track returned to optimal conditions with only a few minutes remaining and Dovizioso recorded a time of 1:49.272 with Toni Elias of LCR Honda and Ducati's Valentino Rossi second and third respectively.