Bezzecchi, racing for Valentino Rossi's VR46 Ducati satellite team, was 0.044sec faster than Spanish Aprilia rider Maverick Vinales with Bagnaia 0.288sec off the pace.
Bezzecchi, looking to bounce back after crashing out of the British MotoGP at Silverstone, put pressure on world championship leader Bagnaia.
Bagnaia has a 41-point lead on Spain's Jorge Martin, who was sixth fastest, in the overall standings with Bezzecchi third, a further six points behind.
France's Fabio Quartararo, the 2021 world champion, clocked the fifth fastest time.
Among those relegated to Q1 was former world champion Marc Marquez, with the Honda rider in 13th position.
The top 10 from practice are joined as usual by the fastest two riders from Q1 to determine the first four rows of the grid both for Saturday's sprint race and Sunday's main event.
