The Italian suffered the injury while training on his flat track bike at Valentino Rossi’s Motor Ranch in Tavullia on Saturday.
He underwent surgery on Sunday at the University of Modena and Reggio Emilia’s Orthopedics and Traumatology Unit.
It is currently unclear whether Bezzecchi, who is third in the championship standings, will take part in next weekend’s Indonesian Grand Prix.
In a statement, the team said: “Successful surgery for Marco Bezzecchi this morning to reduce the fracture in his right collarbone.
“The rider of the Mooney VR46 Racing Team crashed yesterday in the usual training session at the Motor Ranch in Tavullia.
“Marco reached the Orthopedics and Traumatology Unit at UNIMORE where the Team coordinated by Professor Porcellini performed the operation to reduce the lesion.
“The operation was successful.
“Marco will begin the rehabilitation process immediately: his return on track will be evaluated in the next 48 hours.”
The incident will prove a setback for Bezzecchi’s title hopes, as he currently sits on 265 points in the standings - 54 behind factory Ducati rider Francesco Bagnaia and 51 behind Pramac’s Jorge Martin.
Despite the small gap to the leaders, Bezzecchi believes “the real fight” in the championship race does not involve him, saying he is “just running close to them, but never close enough.”
Next weekend’s race in Lombok is the first of a triple header, followed by the Australian GP and the Thai GP at Chang International Circuit at the end of the month.
His injury comes after team-mate Luca Marini also fractured his collarbone in a collision with Bezzecchi in a sprint race shunt at the Indian GP.
Marini suffered a left collarbone fracture, forcing him to sit out the main race in India and the following week’s Japanese GP.
He hopes to return in Indonesia, as does Gresini rider Alex Marquez, who suffered three rib fractures in the same race and also missed the Motegi weekend.
Ducati factory rider Enea Bastianini will also hope to race next weekend, having been recovering from multiple fractures he suffered in a Turn 1 pile-up at the Catalan Grand Prix
Alex Rins will also attempt to make his comeback for LCR Honda, having been sidelined by injury since June's Mugello round with a broken right leg.
He made a brief return at Motegi but suffered too much pain during Friday’s practice sessions and was ruled out of the remainder of the weekend.
