The 31-year-old was eight-tenths of a second quicker than fellow Spaniard and Red Bull GasGas Tech3's 20-year-old rookie Pedro Acosta. Twice MotoGP champion Francesco Bagnaia, the world championship leader, completed the front row.
The pole was the 94th of Marquez's career and second of the season.
"I feel super good and this is the most important," Marquez said. "It's true that the eight tenths looks a lot, but we cannot forget that in other race tracks I was eight tenths behind the pole.
"Now we need to manage our confidence and keep the same mentality because the track is quite slippery and it's easy to make mistakes. So, let's see if we can concentrate in a good way."
Championship contender Jorge Martin came fourth after crashing early in the second qualifying session in Alcaniz. Marquez's brother and team mate Alex was fifth.
Enea Bastianini, third in the championship, had a frustrating morning after the Italian Ducati rider finished fourth in the first qualifying session. He will start 14th in Saturday's sprint and the race on Sunday.
