The Spaniard, who endured a forgettable 2025 season plagued by crashes and injuries, overtook race leader Bezzecchi with three laps remaining to secure his first win since capturing the 2024 title.
"It's unbelievable. I still can't say it enough times, because I'm so, so, grateful to all the fans," an emotional Martin said.
"But for sure I have to remember my family, my team, my girlfriend, my dog - all the people that were with me all this time. I don't have words!"
The victory moved Martin to within one point of championship leader Bezzecchi.
Ai Ogura completed the podium in third for Aprilia's satellite team, Trackhouse, giving the Italian manufacturer its first-ever podium sweep while he became the first Japanese rider on the podium in 14 years.
"What can I say, it just feels amazing... It was not an easy race, but good race pace, and I'm super happy," Ogura said.
Ducati had another Sunday to forget with reigning champion Marc Marquez missing the race after fracturing his foot in Saturday's sprint crash, while teammate and polesitter Francesco Bagnaia crashed in second place.
Bagnaia had a poor start, allowing Bezzecchi to take the lead while home favourite Fabio Quartararo moved up to second.
Martin, unlike his lightning start in Saturday's sprint, where he jumped from eighth to first in two turns, could not make up places initially amid heavy traffic.
But the dynamics shifted dramatically when Bagnaia, who had worked his way up to challenge for the lead, crashed at turn three on lap 16 while under pressure - his third Sunday retirement in five rounds this season.
Martin hunts down Bezzecchi
Martin seized the opportunity, moving past KTM's Pedro Acosta to second and then methodically hunting down Bezzecchi.
Despite trailing by nearly three seconds at one point, Martin chipped away at the gap as the sun emerged from the clouds at an overcast Le Mans.
Acosta's hopes of a third podium finish disappeared with four laps remaining when the late-race specialist Ogura slipped past the KTM rider, setting up Aprilia's historic sweep.
Aprilia boss Massimo Rivola could barely watch as the two factory riders battled for the lead.
With the duo separated by a point after five rounds, he was not worried about any tension between them in the garage, saying: "They are smart people, they are fighters. As long as they respect each other, I'm fine."
As Martin took the chequered flag, he celebrated his breakthrough victory with his trademark windscreen smash before mimicking France forward Kylian Mbappe's goal celebration, crossing his arms across his chest.
"I'm still thinking about last year in Le Mans here, when Jorge wanted to leave (Aprilia), and I said, 'I think you can win with us.' So winning in Le Mans is quite special for me," Rivola added.
In a final twist, Acosta was denied fourth place at the death when VR46 Racing's Fabio Di Giannantonio made a late lunge to steal the position with two corners remaining.
