Andrea Dovizioso topped a mostly irrelevant second practice at Mugello, where the rain meant the majority of the field did not even set a time until the final minutes.
Unlike the morning session, which took place under clear skies, the afternoon was covered by clouds, with rain leaving the riders unable to use slick tyres for most of the event.
However, the circuit wasn't wet enough for teams to want to try wet-weather tyres and most of the field did not even venture out during the first 35 minutes.
Only Randy de Puniet, Hiroshi Aoyama and Toni Elias set a time during the first 40 minutes of the session.
De Puniet led for most of the day, but Elias moved to the top with some eight minutes to go, when several riders jumped onto the track after saying in their garages for most of the afternoon.
Elias showed the track conditions were improving by going some 10 seconds faster than de Puniet, with Dovizioso, using slicks, jumping up to first with less than five minutes to go as the times continued to tumble.
The Honda rider improved even further as the session finished, the Italian finishing on top, over 2.5 seconds ahead of Elias.
Valentino Rossi was one of the first men to jump onto the track after enduring a difficult first session, with both his bikes hit by electrical problems, but the Italian returned to the pits right away to stay there until there were seven minutes left, when he returned to the track.
The Ducati rider was third quickest after just six laps.
Honda's Dani Pedrosa and Casey Stoner, Gresini's Marco Simoncelli and Yamaha's Jorge Lorenzo did not even leave the pits.
Pos Rider Team Time Laps
1. Andrea Dovizioso Repsol Honda Team 1m49.272 6
2. Toni Elias LCR Honda MotoGP 1m51.937s + 2.665 10
3. Valentino Rossi Ducati Team 1m52.550s + 3.278 6
4. Alvaro Bautista Rizla Suzuki MotoGP 1m54.497s + 5.225 4
5. Randy De Puniet Pramac Racing Team 1m55.279s + 6.007 13
6. Karel Abraham Cardion AB Motoracing 1m58.334s + 9.062 2
7. Hector Barbera Mapfre Aspar Team MotoGP 1m58.748s + 9.476 8
8. Cal Crutchlow Monster Yamaha Tech 3 1m59.812s + 10.540 2
9. Nicky Hayden Ducati Team 2m06.386s + 17.114 2
10. Hiroshi Aoyama San Carlo Honda Gresini 2m09.337s + 20.065 3
11. Colin Edwards Monster Yamaha Tech 3 2m10.026s + 20.754 2
12. Ben Spies Yamaha Factory Racing 2m26.938s + 37.666 2
13. Jorge Lorenzo Yamaha Factory Racing No time
14. Dani Pedrosa Repsol Honda Team No time
15. Casey Stoner Repsol Honda Team No time
16. Marco Simoncelli San Carlo Honda Gresini No time