McLaren's Australian rookie Oscar Piastri (22) joined the Formula One world championship leader on the front row with a lap only 0.011 seconds slower than Verstappen's one minute 49.056 seconds.
Ferrari's Carlos Sainz (28) and Charles Leclerc (25) will share the second row.
The standalone sprint format is being used at Spa for the first time, the third of six such events this season.
"It was really difficult, quite similar to yesterday," said Verstappen, who was fastest in every stage and also in Friday's damp-to-dry qualifying for Sunday's main grand prix.
He will start that longer race from sixth place due to a grid penalty.
"The gap was not as big as yesterday but there was also no need to risk it. Probably my second sector was a bit careful, but still on pole. That's what counts," he added.
Piastri said he "couldn’t have got much more out of that" and was happy to be on the front row.
McLaren's Lando Norris (23) qualified fifth fastest with Alpine's Pierre Gasly (27) sixth and Mercedes' seven-time world champion Lewis Hamilton (38) seventh.
The provisional pole changed hands swiftly in the final shootout, with Hamilton fastest then Red Bull's Sergio Perez (33), Gasly, Sainz and Piastri before Verstappen's predictable final flourish.
"It's good to get a clean end to qualifying," said Verstappen, with more rain forecast later. "I think clear vision is going to be very important if it's wet."
The Dutch driver is 110 points clear of Perez, who starts eighth, and he can extend his lead in the sprint with points for the top eight.
Alpine's Esteban Ocon (26) in ninth and Mercedes' George Russell (25) completed the top 10 with AlphaTauri's Australian Daniel Ricciardo (34) 11th.
Hamilton and Russell got in each other's way at the end of the session, with the former saying poor communication had denied him a much better lap.
"We got to the last corner and there were seven cars trundling around," he said.
The session started 35 minutes late due to the weather, with the sprint start also now set to be pushed back due to the gap required by the rules, with the rain then easing off and the sun coming out.
Aston Martin's Lance Stroll (24) halted proceedings in the second phase when he gambled on being the first driver to switch to slick medium tyres and crashed with 29 seconds remaining on the clock.
The accident meant plenty of work for his mechanics while teammate Fernando Alonso (41), who had yet to set a time, also failed to go through to the third and final top 10 phase and will start 15th.
