The race, which took place in wet conditions, was one of the most eventful in years, with outsiders like Marco Melandri and Loris Capirossi having a spell in the lead before Stoner took charge.
Stoner's victory in his Ducati team's home race saw him return to the top of the championship standings.
He now leads Lorenzo by four points, with Rossi a further five points adrift in third, but fourth-placed Pedrosa now looks to be out of the race after another painful crash which looked to aggravate the hip injury he sustained on Saturday.
Stoner was understandably delighted with his victory, but played down the significance of being top of the championship standings.
"At this stage it's not the most important thing," he said.
"Points are always points and as many as you can get is important, but as for the standings, I think it's more the middle to the end of season when it becomes crucial."
Stoner delighted after problematic race
The next race is in Barcelona, where Stoner has done well in the past, and he said he was looking forward to going there again.
"We've had two podium places there in the last two years and I've always enjoyed it," he said.
"Faster tracks suit our bike a bit better and the higher corner speed there makes the bike less aggressive when it starts to move.
"The tracks from now to end of the season are better for us and I think we're going to enjoy ourselves a lot more."
Italian MotoGP race result:
1 C Stoner (Aus) Ducati 45:41.894 2 J Lorenzo (Spn) Fiat Yamaha 45:42.895 3 V Rossi (Ita) Fiat Yamaha 45:43.970 4 A Dovizioso (It) Repsol Honda 45:44.023 5 L Capirossi (Ita) Rizla Suzuki 45:45.168 6 C Edwards (US) Tech 3 Yamaha 46:06.345 7 J Toseland (GB) Tech 3 Yamaha 46:07.515 8 R de Puniet (Fr) LCR Honda 46:07.940 9 N Canepa (Ita) Ducati 46:13.709 10 C Vermeulen (Aus) Rizla Suzuki 46:16.708 11 M Melandri (Ita) Kawasaki 46:16.984 12 N Hayden (US) Ducati 46:21.016 13 M Kallio (Fin) Pramac Ducati 46:34.356 14 T Elias (Spn) Gresini Honda 46:34.372 15 A de Angelis (RSM) Gresini Honda 46:34.967
World championship standings:
1 C Stoner 90 points 2 J Lorenzo 86 3 V Rossi 81 4 D Pedrosa 57 5 A Dovizioso 56 6 M Melandri 48 7 C Edwards 45 8 L Capirossi 38 9 C Vermeulen 37 10 R de Puniet 34
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