Red Bull's double world champion coped best with a Zandvoort circuit hit by heavy rain forcing his thousands of fans to don their plastic ponchos.
Verstappen, 25, seeking to match Sebastian Vettel's record of nine consecutive wins on Sunday, was just under fourth tenths of a second quicker than George Russell for Mercedes, with Sergio Perez in the other Red Bull in third.
Fernando Alonso's Aston Martin, and Lewis Hamilton in the other Mercedes completed the top five.
McLaren's Lando Norris, who had bettered Verstappen in Friday second practice, came in 10th, one place behind Charles Leclerc, the fastest of the two Ferraris.
The storm had eased off before third practice got underway but showers and squally conditions returned, rendering the unforgiving seaside track even more treacherous.
The final session before qualifying later was only a handful of minutes old before the fourth red flag of the weekend came out.
And it was the troublesome turn three that was the centre of attention again as Kevin Magnussen spun his Haas on an 'out lap' at the same spot where Daniel Ricciardo broke his hand on Friday.
The well-positioned crane, already called into action to remove the cars of Ricciardo, Oscar Piastri and Nico Hulkenberg on Friday, extricated Magnussen's stricken vehicle with the action resuming.
It didn't last long though with Zhou Guanyu the next driver to stop the session, his Alfa Romeo coming to rest in safety gravel at turn 13.
"I'm beached guys, it as really wet there," the Chinese driver told his team.
As Zhou's car was removed the timesheets told a familiar tale with the man for all seasons Verstappen leading Norris, fastest in Friday second practice, and Leclerc.
The stop-start session resumed with Leclerc's teammate Carlos Sainz's car taking exception to turn one, the Spaniard doing well after locking up to avoid the gravel.
With the rain letting up Norris went quickest, Verstappen briefly the filler in a McLaren sandwich as Piastri went third.
The third red flag of the session came when Alpha Tauri's reserve driver Liam Lawson, called up to replace the injured Ricciardo, ended up facing the wrong way after a spin but the New Zealander did well to just brush the barrier to keep his car going to return to the pits for a mechanical medical.
The green light came on with eight minutes to go, drivers emerging just as the rain relented as the times tumbled and Verstappen rose to the top.
