Verstappen posted a 1min10.727s flying lap to beat Ferrari rival Charles Leclerc to pole position at Interlagos in a shootout that was red-flagged owing to a thunderstorm hitting the track.
While Q3 was almost entirely dry until the stoppage with four minutes to run, Verstappen reckoned changing wind conditions created "terrible" laps as grip levels disappeared.
McLaren racer Oscar Piastri was caught out by the new-found instability as he lost the rear end of his McLaren MCL60 into the final corner. The Australian rookie had been a credible pole contender after setting the best first sector of anyone.
But as he ran over the grass to trigger yellow flags, the closing Perez was forced to back off from his final flying lap, which he reckons would have put him on the front row alongside his team-mate.
Perez said: "We were just incredibly unlucky today. I should have been on the front row.
"My lap was very close to Max's until the last corner, and I found Piastri so I had to back off my lap.
"It meant that I was just position-nowhere. It's very unfortunate because I felt like we had a lot better."
Source: Autosport