McLaren's Piastri had been on top of the timesheets until the final seconds when double world champion Verstappen went 0.11 quicker with a lap of one minute 49.056 seconds on a drying track.
The standalone sprint format is being used at Spa for the first time, the third of six such events this season.
Piastri said he "couldn’t have got much more out of that" and was happy to be on the front row.
The provisional pole changed hands swiftly in the final shootout, with Hamilton fastest then Red Bull's Sergio Perez, 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.
Persons:
Max Verstappen, Stephanie Lecocq, Perez, Max Verstappen pipped, Oscar Piastri, McLaren's Piastri, Verstappen, Ferrari's Carlos Sainz, Charles Leclerc, Piastri, McLaren's Lando Norris, Alpine's Pierre Gasly, Mercedes, Lewis Hamilton, Bull's Sergio Perez, Gasly, Sainz, Alpine's Esteban Ocon, Mercedes George Russell, Daniel Ricciardo 11th, Russell, Aston, Lance, Fernando Alonso, Christian Radnedge
Organizations:
Belgian, Prix, Spa, Ferrari, Sunday's, Hamilton, Thomson
Locations:
Spa, Belgium