Marquez first set a lap record at the Portimao circuit to top Q1 and breeze into Q2 along with local favourite Miguel Oliveira (28).
But the lap record lasted barely a few minutes as Jack Miller (28) went faster on his new Red Bull KTM machine.
"I can't explain, I do not understand the situation. Yesterday we were struggling a lot but today we improved the small details and I improved myself," Marquez said in a pit lane interview.
"But to do a very fast lap for Honda we need a slipstream," he added, admitting that it was not ideal but necessary. "I feel like for the race distance it will be difficult."
The Australian rider, who made the switch from Ducati prior to the season, sensed it may not be enough and went out again, only to crash at turn three just as reigning champion Francesco Bagnaia (26) broke the record.
But six-times champion Marquez was not done yet and just as the session wound down, the Spaniard put his head down and - with a help of a tow from Enea Bastianini (25) - set the fastest lap with a time of 1:37.226.
Marquez will be joined on the front row with Bagnaia and Pramac Racing's Jorge Martin (25) while Oliveira starts fourth with Miller and Bastianini alongside him.
Former champion Joan Mir (25), who made the switch from Suzuki to Honda, failed to advance from Q1 and will start 14th on the grid.
