But the Dutchman locked up in the final corner and crashed into the wall, ending his hopes of pole. He will start the race third.
Valtteri Bottas completes the front-row, with Mercedes having control as qualifying turned out superbly well for them.
Charles Leclerc was fourth fastest, with Sergio Perez fifth as Red Bull suffered a hit to their hopes in both world championship battles.
Verstappen leads Hamilton by eight points, with Mercedes five points ahead of Red Bull in the constructors championship.
Lando Norris produced a good Q3 display to finish seventh for McLaren, with his teammate Daniel Ricciardo finishing 11th and unable to make the final qualifying session.
Carlos Sainz had a day to forget for Ferrari, and will start the race in 15th after going off the track three times in Q2.
Hamilton did well to keep his focus on events on the track, after an eventful afternoon ahead of qualifying in Jeddah.
The Brit was summoned to the stewards, both for not respecting double waved yellow flags in final practice and also for impeding Haas’ Nikita Mazepin in the same session.
There was no further action for the yellow flags, while he was given just a reprimand for nearly crashing with Mazepin. Mercedes were fined €25,000 for the incident, after not informing Hamilton how close the Haas was to him.