The race was effectively decided when Verstappen overtook Hamilton on Lap 53 of 56 but went too wide on a turn and off track limits.
Verstappen still had a few laps to catch Hamilton and he almost did, finishing .74 seconds behind the Mercedes driver.
Verstappen took a superb pole position on Saturday, the fourth of his career, and started immediately ahead of Hamilton under floodlights at the desert track.
Hamilton was 1.5 seconds behind Verstappen when Mercedes took the bold strategy to switch him to hard tires on Lap 14.
Bottas came in for the same tire change three laps after Hamilton, and Verstappen came in on Lap 18 but again for medium tires.