Both Lowes and Gardner ran close to one another on the final lap, but the former resisted pressure from the Ajo KTM rider to strengthen his championship lead.
Marco Bezzecchi jumped Poleman Lowes off the line, with the VR46 rider holding the Briton in check on the first lap while Ajo KTM rookie Raul Fernandez moved up to third ahead of teammate Gardner.
The pace of the top quartet was so high that on lap three they were 1.7 seconds behind the rest of the field.
Lowes took his step for the lead in the slipstream on the run to Turn 1 early on lap four, while Gardner made a risky – but successful – attack on Fernandez on Turn 10.
The gap between Lowes and Bezzecchi immediately opened to six tenths, with Gardner quickly finishing the Italian on lap six at Turn 1 to begin his hunt for the lead.
Lowes didn’t look as good on his Marc VDS Kalex as he did a week ago, but managed to stop Gardner.
After settling into his rhythm, Lowes felt more comfortable on his bike in the middle distance, although Gardner regrouped in the final stages to put pressure on the leader.
Lowes reacted emphatically to this threat, the Marc VDS driver shot three laps before the end in a race best time of 1: 59.026 minutes and extended his lead to over half a second.
Gardner dug deep to keep Lowes in his crosshairs, the Ajo rider improved on the penultimate tour with 1: 58.991 minutes on Lowes’ fastest lap.
The pair ran line aft in the final corners of the race, Gardner tried to make a move at turn 15 but couldn’t find a way.
Lowes covered his line on the way to the last corner, a small moment of acceleration for Gardner allowed the Marc VDS driver to cross the checkered flag with a 0.190 second lead.
Fernandez took a comfortable first place on the podium on the sister Ajo bike after beating Bezzecchi, while Honda Team Asia rookie Ai Ogura finished an impressive fifth.
Augusto Fernandez finished sixth on the second Marc VDS Kalex, Celestino Vietti put another impressive rookie performance on the VR46 Kalex with seventh place ahead of Pons’ Stefano Manzi, Xavi Vierge (Petronas Sprinta) and Gresini’s Fabio Di Giannantonio.
Joe Roberts (Italtrans) crashed from fifth at the start of the race, while compatriot Cameron Beaubier was retired on his second Moto2 start for American Racing.
Jake Dixon from Petronas Sprinta was involved in a collision with Marcel Schrotter from Intact GP, while Tom Lüthi (SAG), Aspars Aron Canet and MV Agusta representative Tommaso Marcon were also out.
Lowes goes to the third round of the season in Portugal in two weeks and leads the championship by 10 points over Gardner.