The double Formula One world champion, who will be chasing a record-equalling ninth win in a row on Sunday, lapped the seaside circuit with a best time of one minute 21.631 seconds on a drying track at the end of the session.
Verstappen has won his home race from pole position each time since its return to the calendar in 2021 and is favourite to complete his hat-trick and stretch his lead over teammate Sergio Perez (33) from a current 125 points.
Mercedes' George Russell (25) was second fastest for Mercedes with a lap 0.379 slower, while Perez was third and a second off the pace.
A string of drivers, including Verstappen, ran wide in tricky conditions before the rain eased off.
Kevin Magnussen (30) brought proceedings to a halt after 10 minutes when he spun his Haas at turn three and ended up stranded on track with a damaged front left suspension.
Alfa Romeo's Guanyu Zhou (24) beached his car in the gravel at the penultimate corner with 35 minutes to go, bringing out red flags again.
AlphaTauri debutant Liam Lawson (21) then halted the track action when he spun with 12 minutes remaining and was left facing the wrong way.
The New Zealander, replacing Daniel Ricciardo (34) after the Australian broke his hand in a crash on Friday, got the car going again and ended up 18th.
