Marquez had initially topped Q1 to move into Q2, but he had to switch bikes after his machine caught fire after a fall, and he had to abandon it on the side of the track as marshals extinguished the flames licking the bottom of the bike.
But as the track began to dry up, several riders switched to slick tyres and Marquez -- who hitched a ride back to the paddock -- capitalised to take pole right at the end to start up front for the sprint later on Saturday and for Sunday's race.
"I'm super happy, Q1 was so difficult with the wet tyres and I made a mistake in the penultimate corner... Later on I had the problem with the fire," Marquez said in a pit lane interview.
"I did my best with the wet tyres. Later on I go in I thought there was no time to change the tyres. But we changed the tyres... and it was working, so really happy for that and looking forward to the sprint and the race."
Ducati's Francesco Bagnaia, who leads the championship after his sprint-race double victory in Portugal last weekend, was one of the first riders to switch to slick tyres towards the end of the session but he could only take third on the grid.
"Considering the number of wet patches, it was very risky (switching tyres). But I'm very happy... Let's focus on the race but these conditions are very tricky," Bagnaia said.
The reigning champion will start alongside VR46 Racing's Marco Bezzecchi who was second fastest.
Yamaha's Franco Morbidelli was initially the fastest man on the wet tyres but will now start fourth on the grid, while his team mate Fabio Quartararo struggled, finishing the session 10th fastest.
Maverick Vinales of Aprilia, who dominated Friday practice, was fifth fastest while Johann Zarco of Pramac Racing completes the second row.
Alex's brother Marc is not racing this weekend after the Honda rider and six-time MotoGP champion injured his hand in a crash at the season opener in Portugal.
