Red Bull's championship leader was down in fifth after the first barrage of Q3 runs. Amid scintillating pole bids by Esteban Ocon, Charles Leclerc and Alonso, Verstappen then had the last word as the chequered flag dropped.
Despite two personal bests he was still trailing Aston Martin driver Alonso heading into the final sector, but with a stunning recovery his 1m11.365s effort pipped the Spaniard at the line by 0.084 seconds.
Verstappen was seen brushing the pit straight wall on his way to pole and later revealed he "clipped a few barriers" on his way to his first-ever pole in the principality.
"My first sector was not ideal on my final lap, I think Turn 1 was a bit cautious," he said.
"But then I knew I was behind, so the last sector I gave it everything I had, clipped a few barriers but of course very happy to be on pole here for the first time.
"We knew that this was going be a bit of a struggle for us to get everything together, yesterday was not the best start but we kept on improving and kept on being better. But then in qualifying you need to go all out and risk it all."
Source: Autosport