Martin took the chequered flag 1.445 seconds ahead of VR46 Racing's Bezzecchi to claim his third sprint win of the season. World champion Bagnaia finished third.
Bagnaia is top of the riders' standings with 267 points, with Martin (222) in second and Bezzecchi (196) in third. Martin's sprint win reduced the gap to Bagnaia by five points, while Bezzechi's second-placed finish saw him reduce the deficit by two.
"I expected the first few laps to be more difficult, but then Marco pushed a lot and I had to be at the absolute limit all the time," Martin said.
"Hopefully tomorrow I'll feel a little bit stronger."
Spaniard Martin, who set a lap record in qualifying to take pole, made a blistering start as he rocketed off the line and sped away from his pursuers, building a gap of half a second over Bagnaia at the end of the first lap.
After Bezzecchi recovered from a slow start to leapfrog Bagnaia, Martin was given more of a challenge, though the Spaniard proved triumphant.
"It was very difficult, but we are in Misano, so I had to be strong and give a good show to the fans," said Bezzecchi, who is nursing a wrist injury after being involved in a crash last week.
Bagnaia, who was also carrying an injury after having his leg run over in a crash at the Catalan Grand Prix, was drawn into an intense battle for third with wildcard Dani Pedrosa but managed to hold off the veteran.
"It's something incredible (to finish third), considering the pain I felt while riding. The feeling during the race wasn't happy, but I'm always happy to be on the podium," Bagnaia said.
"I want to say congratulations to Jorge. He did a great job."
Aprilia's Maverick Vinales and Aleix Espargaro finished sixth and eighth, on either side of Bezzecchi's teammate Luca Marini - whose mentor and MotoGP great Valentino Rossi was watching from trackside.
Yamaha's Fabio Quartararo, the 2021 world champion, finished 13th while six-time MotoGP champion Marc Marquez ended in 10th.
Italian Enea Bastianini of Ducati, who underwent surgery in Modena on Monday after fracturing his left hand and ankle at the Catalunya GP, will miss Misano as well as races in India and Japan.
