Countrymen Rossi and Marco Melandri - second to Lorenzo at Le Mans and second to Casey Stoner in this morning's wet warm-up - were also in hot pursuit, the #46 rising swiftly through the lead group to take the lead from Dovizioso on lap eight.
Melandri demoted Dovi from second soon after then, on lap ten, made a move unthinkable at the start of the year - overtaking Rossi for the lead of his home grand prix!
Meanwhile, James Toseland had been the first rider to gamble on changing bikes, the Briton diving into the pits at the end of lap four - and by lap eight he was the fastest man on track.
Dovizioso was the first of the frontrunners to pit on lap nine and at the end of lap ten the four leading riders - Melandri, Rossi, Lorenzo and Stoner - did likewise.
Melandri's Hayate emerged back in the lead, but Dovizioso was already up to full racing speed and carved his way to the front by 2.9sec over Stoner by the end of the lap, with Melandri third, Lorenzo fourth, Loris Capirossi fifth and Rossi sixth.
Former Ducati team-mates Stoner and Capirossi - running the softer compound slicks - then emerged as the men to beat; Stoner retaking the lead from Dovizioso with ten laps to go, then losing out to Capirossi's Suzuki.
Suzuki have not had a rider finish on the podium at Mugello since Daryl Beattie was second in 1995, but Loris looked to be gunning for a repeat of his 2000 500cc Mugello win for Honda.
The constantly drying track may have been working against the GSV-R, but only Stoner had got past Capirossi with two laps to go; whereupon the #65 fell victim to both Lorenzo and Rossi.
The last lap began with Lorenzo less than one second from Stoner, with Rossi a further second back. Any hopes of a miraculous last lap by Rossi to snatch an eighth consecutive home victory were soon dashed as the reigning six time MotoGP world champion instead found himself under pressure for the final podium position from Dovizioso.
Rossi held on by just 0.053sec at the flag and the visibly disappointed Italian joined a delighted Stoner and Lorenzo on the podium. Dovi thus lost out on his first rostrum of the year by one place for the second race in succession, while Capirossi dropped to the tail of the group in fifth.
But Dovizioso's fortunes were far better than team-mate Pedrosa.