In a pulsating, see-sawing qualifying session around the famous streets of Monte Carlo, Alonso was seconds away from claiming his first pole in over a decade until an incredible last-gasp effort from Verstappen.
Verstappen remarkably found two tenths in the short final sector and survived a hit with a barrier coming out of the final corner to snatch his first pole in Monaco, beating Alonso by just 0.084s.
It marked the two-time world champion’s 23rd career pole and was arguably the finest of his career to date.
Home favourite Charles Leclerc missed out on a third consecutive pole by 0.106s and had to settle with third place, but the Ferrari driver faces an investigation for a potential block on Lando Norris.
Alpine’s Esteban Ocon briefly held provisional pole with an incredible lap that was good enough for fourth, ahead of Ferrari’s Carlos Sainz.
Lewis Hamilton was three-tenths off the pace as he took sixth in his upgraded Mercedes, ahead of the second Alpine of Pierre Gasly and teammate George Russell.
Yuki Tsunoda and Norris completed the top-10 order for AlphaTauri and McLaren respectively.
It was a calamitous qualifying session for last year’s winner Sergio Perez, who slammed into the wall at Sainte Devote in Q1, leaving him 20th on the grid and last.
It marks a potentially devastating blow to Perez’s title hopes, with the Mexican already 14 points behind his teammate and needing a miracle to avoid a further points loss on Sunday.