Marquez, who is second in the season's standings behind champion and brother Marc Marquez, has won two sprint races in a row. KTM's Acosta, who was more than 1.4 seconds behind with four laps to go, tried to make up some ground but ended 1.149 seconds slower.
Alex, who won the Spanish Grand Prix and the Catalonian Grand Prix earlier this year, will be looking to win a third straight race on home soil as the 2025 season comes to an end at Circuit Ricardo Tormo on Sunday.
"I tried my best to attack from the start. The key was to put our rhythm, save a little bit of time in the beginning and then push in the end," said the Spaniard.
VR46 Racing's Fabio Di Giannantonio came in third, 2.637 seconds behind Alex Marquez, while Raul Fernandez narrowly beat Marco Bezzecchi to finish fourth.
Bezzecchi, who took pole position in qualifying earlier in the day, has secured third place in the championship, the first for an Aprilia rider.
Alex passed Bezzecchi early in the race to take the lead, with Acosta giving chase. The pair had opened up a gap of more than 1.4 seconds to the rest of the riders by the sixth lap.
Acosta said he was happy with his performance despite not being able to match compatriot Alex's speed.
"This is like a football match, when you are trying to take a penalty," said Acosta, who is fourth in the championship, six points ahead of Francesco Bagnaia.
Last year's champion Jorge Martin, making his comeback after nearly five months out with a serious injury suffered during training, finished last, while Honda teammates Joan Mir and Luca Marini crashed out after a collision in the second lap.
Marc Marquez ended his season early after suffering a collarbone injury at the Indonesian Grand Prix last month, a week after winning his seventh premier-class crown at the Japanese Grand Prix.
