Starting second on the grid, Fernandez surged into the lead halfway through the opening lap and never looked back, beating Martin by more than a second after the factory rider had cut the gap with three laps remaining.
VR46 Racing's Fabio Di Giannantonio completed the podium while championship leader Marco Bezzecchi finished fourth ahead of Ducati's Marc Marquez in fifth.
"I feel super happy, I don't really have the words, but thanks to the team," a beaming Fernandez said.
"Since Jerez we are doing a good job. Today and yesterday (in practice) I felt the pace, I felt comfortable with the bike."
The victory was redemption for Fernandez, who had collided with Martin at the Catalan Grand Prix earlier this month as both riders crashed out, sparking a heated confrontation between team bosses in the garage.
But this time Aprilia boss Massimo Rivola was all smiles as he came over to congratulate their satellite team for a job well done.
Poor getaway for Bezzecchi
The race got off to a chaotic start when pole sitter Bezzecchi had a poor getaway, allowing Marquez to storm off the second row and lead into turn one.
But Fernandez, Martin and Diogo Moreira quickly elbowed their way past the Ducati to push him back down to fourth.
Marquez, who was making his return from double surgery on his foot and shoulder, then lost more positions as Di Giannantonio and Bezzecchi surged past him.
Di Giannantonio quickly moved up to third when he found his way past Moreira, who received a track limits warning before dropping to fifth and finding himself defending his position against Marquez.
Up front, Fernandez appeared to be cruising but Martin found another gear and reduced the gap with every lap until he was less than half a second behind the Trackhouse rider with three laps left.
However, Fernandez managed to surge ahead and take the chequered flag nearly a second ahead of his Spanish compatriot.
"We always try to fight for the podium and this was my target today, I felt great," Martin said.
"When I was closing the gap to Raul, it was becoming a bit more difficult. But finally I thought the points were more important than a crash. I did my best, Raul was impressive."
Fernandez moved up to fifth in the championship standings with the victory while Martin cut Bezzecchi's lead to 12 points ahead of Sunday's race.