Remy Gardner was due to start on pole after Sam Lowes was forced to start from pitlane as punishment for his Styrian GP collision with Jorge Navarro and Somkiat Chantra.
However, Gardner fractured his hand and foot in a heavy crash in warm-up, ruling him out of the race and promoting championship leader Marini to pole.
The VR46 rider grabbed the holeshot ahead of Enea Bastianini, though the Italtrans man was quickly demoted by the sister VR46 bike of Bezzecchi at the Quercia corner at Turn 8.
The VR46 pair immediately opened up a gap to the chasing Bastianini, with the gap up to a second by lap four.
Marini was also putting daylight between himself and Bezzecchi, with a six-tenth gap extending to over a second by lap nine.
Bastianini’s gap continued to open to 1.7s to Bezzecchi ahead, though the gap between the three did start to steadily reduce come lap 16.
Marini was now just seven tenths clear, with Bezzecchi holding eight tenths over Bastianini – though the latter’s charge looked to have come to an end when he had a big front end moment at Quercia on lap 16, which dropped him 2.5s adrift of second.
Bezzecchi continued to put pressure on his teammate, and found himself in the lead at the end of lap 18 when Marini ran wide at the Carro hairpin of Turn 14 due to hitting a false neutral.
The two VR46 riders engaged in a fierce tussle for the lead, with Marini launching a move at Quercia on lap 21.
Bezzecchi drew alongside on the exit and regained the position at the Tramonto right-hander – all of this allowing Bastianini to start closing in again.
Marini made a failed attempt at regaining the lead at Turn 2 on the following lap, but made a move stick at Quercia.
A mistake for Bezzecchi at Carro on the penultimate tour gave Marini 1.1s of breathing space to secure his second win of the season.
Bezzecchi fended off MotoGP-bound Bastianini by 0.098s to secure a VR46 1-2, while Petronas Sprinta’s Xavi Vierge and the Marc VDS bike of Augusto Fernandez completed the top five.
Tom Luthi was sixth and the sole Intact GP bike at the finish in sixth after teammate Marcel Schrotter – who ran third early on – crashed late on.
Speed Up’s Fabio Di Giannantonio was seventh at the chequered flag, with Lowes recovering to eighth on his Marc VDS bike from pitlane ahead of Aspar’s Aron Canet and American Racing’s Joe Roberts.
Marini’s championship lead has extended to 17 points over Bastianini, with Bezzecchi a further 27 points adrift in third.
Absent due to COVID-19, Ajo KTM’s Jorge Martin has slipped to fourth in the standings and 33 points down on Marini.