Portuguese rider Miguel Oliveira was ninth with Fenati's team mate Tonucci also finishing in the top ten. Hector Faubel finished 11th after his massive crash last weekend for Aspar.
British wild card John McPhee featured in the top five early on and despite looking and grabbing at his clutch with an apparent problem still finished in the points in 15th for Racing Steps Foundation.
Louis Rossi did not feature near the front at Brno and finished the race in 17th for Racing Team Germany and Joan Olive was 18th in his stand-in ride for the TT Motion Events team, replacing the banned Niklas Ajo.
Zulfahmi Khairuddin crashed out of fifth place while trying to keep up with Vinales on the AirAsia KTM while Czech rider Miroslav Popov, substituting for an injured Danny Webb on the Mahindra also crashed out with four laps to go.