Capirossi overtook Melandri on the final lap to give Ducati their first podium finish of the year.
BBC: SPORT | Motorsport | Motorbikes | Rossi holds off Biaggi at Mugello
Melandri was neck-and-neck with Nieto on the final lap and held him off by just 0.007s in the home straight.
Marco Melandri and Loris Capirossi should be fit to start in Assen on Saturday, despite suffering injuries in the same incident.
BBC: SPORT | Motorsport | Motorbikes | Rossi aims to race despite crash
Marco Melandri came out on top in a battle with Alex Barros and Nicky Hayden to take the final podium place.
BBC: SPORT | Motorsport | Motorbikes | Rossi snatches win from Gibernau
Meanwhile, Marco Melandri, edged out Fonsi Nieto to win the 250cc race and become the youngest ever world champion in the class.
British rider James Toseland equaled his best finish in MotoGP when he claimed sixth for Edwards' team after Italian Marco Melandri crashed late on.
Incidentally, the only rider to have won races in all three classes here is Marco Melandri, who was 14th fastest on Friday on the Hayate.
Rossi has now won four of the five races this season on the Gauloises Yamaha, and leads Melandri by 49 points in the overall standings.
BBC: SPORT | Motorsport | Motorbikes | Rossi holds off Biaggi at Mugello
It came down to who was feeling good and whose bike felt good underneath them and Melandri emerged as that guy from the word go.
BBC: SPORT | Motorsport | Motorbikes | Melandri's back on track
Rossi now leads Melandri by 58 points in the title race.
BBC: SPORT | Motorsport | Motorbikes | Rossi snatches win from Gibernau
The government reaction has been stronger with calls from the sports minister, Giovanna Melandri, for all football matches to be suspended for the next few weeks.
Le Mans winner Marco Melandri holds a 24-point margin over Rossi in third, while Spanish newcomer Daniel Pedrosa is 21 points ahead of him in fourth.
BBC: SPORT | Motorsport | Motorbikes | Rossi targets Barcelona hat-trick
Melandri led the charge and briefly took over at the front, but it was left to Biaggi to challenge Rossi in the closing stages of the race.
BBC: SPORT | Motorsport | Motorbikes | Rossi holds off Biaggi at Mugello
Elias and Alex de Angelis will be replaced by Marco Simoncelli and his fellow Italian Marco Melandri, who returns to the team he raced for from 2005-07.
The 27-year-old Melandri was runner-up in the world championship in 2005 but was less successful last year with Ducati and has done well with limited resources at Hayate this season.
Italian pair Loris Capirossi and Marco Melandri will be there or thereabouts, however I have a suspicion that Stoner might get the better of his new team-mate at Ducati, Capirossi.
BBC: SPORT | Motorsport | Motorbikes | Steve Parrish's MotoGP Column
Trying to predict this race is very difficult - you might as well close your eyes and stick a pin on any one of Melandri, Capirossi, Rossi, Hayden or Pedrosa.
BBC: SPORT | Motorsport | Motorbikes | Melandri's back on track
Spies returned in second to last place, ahead of Hayden, but picked off Mika Kallio, Hiroshi Aoyama, Marco Melandri, Aleix Espargaro, Hector Barbera and Randy de Puniet to seal an impressive eighth place.
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.
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