The fight for fourth was the only contest to stay alive to the flag, with Marco Melandri, Randy de Puniet and 2009 Mugello winner Casey Stoner trading places for much of the race.
Stoner secured fourth - his best result of the season - with a last lap pass on Melandri's Gresini Honda, while LCR Honda's de Puniet was left to settle for sixth, having led the group on the penultimate lap.
Ben Spies, who ran as high as fourth in the early laps, lost touch with the trio ahead on the final lap, but seventh place was just the kind of solid race he needed after failing to reach the flag in the past two events.
It will also do his chances of being called up to replace Rossi no harm at all, especially since Monster Yamaha Tech 3 tam-mate Colin Edwards - favourite for the temporary promotion - sunk back to 13th in the race.
Rossi is likely to be replaced by Catalunya at the latest, which follows Silverstone and Assen on July 4.
Stoner was the only Ducati rider to finish after team-mate Nicky Hayden suffered his first DNF of the year, the American sliding out of sixth on lap six. Another Desmosedici rider, Mika Kallio, also failed to finish.
Behind Spies, the top ten was completed by Aleix Espargaro, Marco Simoncelli and Suzuki's Loris Capirossi.
Pramac's Espargaro claimed his best MotoGP finish, while Honda Gresini's Simoncelli charged through the field after running off track on the opening lap.
Italian Grand Prix:
6. de Puniet