The German, who took his second pole position of the season, was almost two-tenths of a second ahead of teammate Charles Leclerc.
Mercedes dominated the timesheets during the practice sessions on Friday, however neither of its two drivers could challenge the Maranello squad during qualifying, which took place hours before the start of the race.
However, as Verstappen set the lap time first, he will start in fifth place and in front of his Thai-British teammate.
Robert Kubica's session ended early as he dipped a wheel onto the exit of the final corner, crashing into the barriers in Q1 and bringing out a red flag.
After his car was cleared, it wasn't long before a second red flag was brought out for Kevin Magnussen, who appeared to be caught out by a gust of wind at the last turn, which pitched him into the wall.
Despite a heavy hit with the barrier, Magnussen drove his Haas car back to the pit lane, but didn't rejoin the track, joining Kubica, George Russell, Sergio Perez and Daniel Ricciardo in the Q1 drop zone.
The Italian once again out-qualified veteran teammate Kimi Raikkonen, who ended Q2 in front of Daniil Kvyat and Nico Hulkenberg, with the latter suffering a hydraulics failure that prevented him from setting a competitive lap time.
Bahrain International Circuit - Winter testing