Reigning champion Bagnaia, who trails Martin by 23 points, sped to one minute and 30.304 seconds at the "Marco Simoncelli" circuit in Misano Adriatico, ahead of countrymen Franco Morbidelli and Marco Bezzecchi who was also fastest in the morning practice session.
Ducati's Bagnaia is riding with injuries to his shoulder, neck and collarbone after crashing out of last weekend's Aragon MotoGP but put himself in position to gain points on Martin.
Spaniard Martin, who rides for Ducati satellite team Pramac, is in the second row for Saturday afternoon's 13-lap spring race and the Grand Prix on Sunday alongside Pedro Acosta and Brad Binder after finishing fourth fastest, 0.341sec behind Bagnaia.
Binder is in sixth place on the grid.
Picture-perfect @PeccoBagnaia! ??
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