Italian Morbidelli was a popular local winner at Misano in front of a limited number of spectators, who were allowed at a race for the first time in 2020 amid the coronavirus pandemic.
The impressive Francesco Bagnaia (Pramac Racing) flew through the pack from sixth on the grid to take second behind Morbidelli, holding on for a first career podium amid a frantic final lap on his first race back since returning from a serious knee injury.
Valentino Rossi (Monster Energy Yamaha), who grew up in the nearby town of Tavullia, looked as though he had done enough to finally land a landmark 200th career podium in third.
But Joan Mir (Suzuki Ecstar) had fantastic race pace throughout and passed Rossi – who must have felt bittersweet as Morbidelli and Bagnaia are graduates of his academy – on the final lap to snare a memorable podium, with both men in pursuit of Bagnaia.
It was a day to forget for Quartararo, though, as the Frenchman – many people's pre-race favourite – tumbled with 14 laps remaining after going too wide at Turn 4.
To compound a miserable day, Quartararo – who had struggled right from the off – later came off the bike again shortly after returning from the pitlane as Dovizioso to moved top of the standings by six points despite finishing back in seventh.
Maverick Vinales had started on pole after a record-breaking lap on Saturday but once again struggled to produce qualifying pace on Sunday.
The Spaniard was jumped on the line by Morbidelli, who celebrated with the Italian flag on a very slow cool down lap, and Rossi before falling back through the pack and finishing sixth.
- Franco Morbidelli (Petronas Yamaha)
- Francesco Bagnaia (Pramac Racing) +2.217s
- Joan Mir (Suzuki Ecstar) +2.290s
- Valentino Rossi (Monster Energy Yamaha) +2.643s
- Alex Rins (Suzuki Ecstar) +4.044s
- Maverick Vinales (Monster Energy Yamaha) +5.383s
- Andrea Dovizioso (Ducati) +10.358s
- Jack Miller (Pramac Racing) +11.155s
- Takaaki Nakagami (LCR Honda) +10.839 (demoted one place)
- Pol Espargaro (Red Bull KTM Factory Racing) +12.030
- Andrea Dovizioso (Ducati) 76
- Fabio Quartararo (Petronas Yamaha) 70
- Jack Miller (Pramac Racing) 64
- Joan Mir (Suzuki Ecstar) 60
- Maverick Vinales (Monster Energy Yamaha) 58
- Petronas Yamaha 127
- Monster Energy Yamaha 116
- Ducati 101
- Suzuki Ecstar 100
- Pramac Racing 97
The teams will not be packing up the equipment just yet as MotoGP™ stays in San Marino for the Emilia Romagna Grand Prix in the coming week for the second leg of a double-header at Misano.