Tomizawa, who was in the fourth position at the time, lost control coming out of a turn and fell on the Misano World Circuit in the 12th lap. He was then run over by two other riders, Italy"s Alex de Angelis and Scott Redding of Britain, in high speed.
He sustained grievous injuries and succumbed at the hospital.
Tomizawa, who competed for the Suter team, is the first rider to die in MotoGP racing since compatriot Daijiro Kato at the Suzuka home race in 2003.
The Suter Racing team was "completely shattered" by the death of the 19-year-old.
"Shoya was more than a friend. He was like a family member," Suter Racing's CEO Eskil Suter said in a statement.
"He was loved by everybody in the paddock and I am terribly sorry for his family and his team who suffered this tragic loss," Suter added.