Martin, who had stormed to the MotoGP pole position ahead of reigning champion Marquez's Ducati earlier on Saturday, finished ahead of Marquez to claim his 20th sprint victory, after KTM's Pedro Acosta crashed out while leading late in the race.
The 28-year-old Martin, the 2024 MotoGP champion, now has 286 points in the standings, three ahead of Spanish compatriot Marquez going into Sunday's Grand Prix at the Red Bull Ring in Spielberg.
Martin's race appeared to unravel in the opening corners when he was forced on to the defensive by seven-time MotoGP champion Marquez, running wide and dropping to eighth on the first lap.
Acosta seized the opportunity to take command and opened up a lead of nearly three seconds, only to crash out with about three laps remaining.
Martin, meanwhile, carved his way back through the pack to secure a remarkable victory.
"I enjoyed the race for sure," Martin said. "I was a bit lucky with Pedro because we thought that I would be second. We started well but then we were on the limit on the first lap, so I thought my chances were over.
"But then, lap by lap, I didn't give up during the race. I was pushing till my maximum, trying to be super concentrated to come from the back and then win. The end was so good.
"I am really happy for my team because they really deserve it. We are ready for tomorrow. I hope that we can continue at this pace."
Aprilia's Marco Bezzecchi, third in the championship standings, completed the podium.
Trackhouse Aprilia's Ai Ogura finished fourth with Alex Marquez fifth.