Pramac Ducati rider Martin was never truly threatened at the head of the field, easing away from the chasing pack over the course of Saturday's 12-lap contest to record his fifth sprint race win of the season.
It means the gap between Martin and works Ducati man Bagnaia is now down to just eight points ahead of the main race on Sunday.
However, Bagnaia managed to gain back a crucial point with a brave pass on Jack Miller to finish third after a poor start from second on the grid.
Bagnaia dropped to fourth on the opening lap as he was passed by the two KTMs of Miller and Brad Binder, who proceeded to swap places at the downhill Turn 11 right-hander.
Binder briefly looked as if he would threaten Martin for the lead, but by the eighth lap he was a second down on the Pramac rider and took the chequered flag just under 1.4s in arrears.
All eyes were then on the battle for third as Bagnaia caught up to Miller and applied the pressure on the Australian in the closing stages.
The decisive move arrived on lap 10, as Miller braked slightly too late at Turn 11, giving Bagnaia the chance to cut to the inside and then sweep all the way around the outside of the KTM man at Turn 12.
Miller managed to hang on to fourth, seeing off a late charge from the second Pramac bike of Johann Zarco.
Marco Bezzecchi was sixth on the VR46 Ducati after passing Honda's Marc Marquez at the Turn 8-9 complex on the penultimate lap.
Fringe title contender Bezzecchi had been running ahead of Zarco until he ran wide at Turn 11 in a failed bid to get ahead of Marquez for fifth on lap eight, allowing not only Zarco but also the Aprilia of Aleix Espargaro through.
However, Espargaro would soon pit to retire his RS-GP with apparent mechanical issues.
That meant the marque's lead finisher was Maverick Vinales, who claimed the final point in ninth behind the solo Gresini Ducati of Fabio di Giannantonio.
The Yamaha contingent endured a miserable sprint as Fabio Quartararo trailed home 15th, with team-mate Franco Morbidelli behind in 16th.
Wildcard Cal Crutchlow was 18th after picking up a long lap penalty for exceeding track limits, one place behind local hero Takaaki Nakagami on the LCR Honda.
Results to follow
