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The first stoppage was for Lance Stroll crashing at Raidillon, with the second for standing water.
Conditions deteriorated as the session wore on, having started damp before closing in.
The weather did not dissuade Verstappen from heading out as the pit lane opened, though he promptly ran wide at Bruxelles on his out lap.
The Dutchman was on the intermediate rubber, seemingly the better-suited tyre for conditions as some opted for the full wet.
Times were some 30 seconds off the dry pace, his initial time a 2:03.232s.
Oscar Piastri was another of those to head out early, looking to get on track before the rain intensified.
In the early minutes, he went second fastest, though in reality times were meaningless given the conditions.
On off for Lando Norris at Malmedy saw the McLaren mechanics working under his car during the Stroll red flag to replace his floor.
Mercedes delayed its entry into the session, missing the best of the conditions in the process.
As Lewis Hamilton and George Russell emerged from the garage, the rain increased, as predicted by other teams.
The RB pit wall anticipated a “big chunk” of rain arriving five minutes into the session, the squad sending Daniel Ricciardo and Yuki Tsunoda out immediately as a result.
Ricciardo reported a suspected hydraulics issue after he experienced heavy steering.
The team saw nothing on the data, but with the Australian insistent and boxed as a precaution.
Stroll crashed at Raidillon after 12 minutes, damaging the left-front wheel of his Aston Martin to draw the red flag and, for all intents and purposes, ended the session.
He stopped just prior to the Kemmel Straight having aquaplaned as he climbed Raidillon, spinning and brushing the barrier on drivers’ left.
It was enough of an impact to see the medical car deployed, though Stroll was able to climb free and walk to the car once it arrived.
The delay lasted nine minutes, though nobody headed out as the session resumed – which it did only briefly before it was red flagged again, this time for standing water.
And so it remained until the FIA resumed the session with two minutes remaining, a decision made to allow cars out on track to perform a practice start.
Carlos Sainz took the opportunity, and skidded off at Bruxelles just as Verstappen had done to start the session, though the Ferrari went further wide and bounced through the gravel and return to the track.
It marked an end to the session as the chequered flag waved soon after to bring running to an end, though it had effectively stopped some 45 minutes earlier.
