Pole-sitter Ai Ogura, who had set a lap record in qualifying, finished 0.241 seconds behind the Italian in Brno. The win was Bagnaia’s first since Sepang last season.
His teammate Marc Marquez climbed from fifth on the grid to complete the podium in third, while VR46 Racing Team’s Fabio Di Giannantonio took fourth place.
Aprilia’s world championship leader Marco Bezzecchi crashed out at Turn Three on lap eight - his fourth sprint retirement of the season.