The Spaniard, who began the race nine points behind Lorenzo but nursing a hip injury sustained in a near-highside on Saturday morning, was flung from his RC212V while holding eleventh on lap 13.
The triple 2009 podium finisher was slow to move and eventually carried away on a stretcher. Pedrosa has now dropped 33 points from the world championship lead, while Rossi has slipped from joint second with Stoner to third, nine points behind the Australian.
Toseland's early bike change saw the Englishman dispute sixth with LCR's Randy de Puniet for much of the second half of the race, before Monster Tech 3 Yamaha team-mate Colin Edwards snatched the position from him on the very last lap.
Behind de Puniet, rookie Niccolo Canepa made good use of his Mugello knowledge to claim a best yet ninth for Pramac Ducati - having also opted for an early bike change after struggling in the wet - while Vermeulen's form went in the other direction and he slipped back to tenth in the dry.
Melandri was another to suffer as the weather improved, crossing the line eleventh, with Nicky Hayden finishing his first Italian Grand Prix for Ducati in twelfth, ahead of Pramac's Mika Kallio.
Gresini Honda riders Toni Elias and Alex de Angelis completed the field. de Angelis remounted after a crash, while Scot Honda's Yuki Takahashi joined Pedrosa in going down and out.
Grupo Francisco Hernando Ducati rider Sete Gibernau is not present this weekend after fracturing his left collarbone at the French Grand Prix.
Italian Grand Prix:
8. de Puniet
15. de Angelis