Miami became the Dutchman's seventh Sprint pole of his career as he finished ahead of Ferrari's Charles Leclerc in second and Red Bull team-mate Sergio Perez completed the top three.
Daniel Ricciardo recorded his best qualifying of the season with fourth for RB, while the McLaren's of Oscar Piastri and Lando Norris could only manage sixth and ninth respectively, having looked liked they could challenge Verstappen for first throughout the day.
And the three-time champion seemed surprised himself that he will line up at the front of the grid for the Sprint on Saturday.
Verstappen stunned by Miami Sprint pole
Speaking over his team radio after the session, Verstappen was stunned to hear that his lap had secured him pole.
"LOL. What happened to the others? This was terrible," he said.
"I mean I will take it!"
Speaking with Naomi Schiff as he stepped out of the car, the Dutchman highlighted his struggles throughout the session.
"It felt really terrible," he said. "Maybe that last session was just incredibly difficult to get the tyres to work.
"Already in SQ2 I didn't feel great. SQ3, it just felt quite similar for me.
"I didn't really improve on the soft. Somehow we were first. Of course, I happily take it.
"But it didn't feel enjoyable out there to drive for whatever reason because in practice it felt really, really nice, I was very comfortable and confident, qualifying, not so much."
"It might be the track layout a little bit. I thought after practice, I was quite confident we could fight for pole, then in qualifying it didn't really look like that for me.
"But somehow we ended up in first. I don't know what happened to the other cars on that last lap."