McLaren's Australian rookie Oscar Piastri and British teammate Lando Norris were second and third fastest, 0.585 and 1.277 seconds respectively slower than Sainz's best effort of two minutes 03.207 seconds on the intermediate tyres.
Ferrari's Charles Leclerc was the quickest driver on wet tyres, fourth on the timesheets, with Red Bull's Sergio Perez fifth.
Heavy spray and poor visibility meant the soaked fans saw little action for their pains.
The session was halted for 10 minutes when Williams rookie Logan Sargeant hit the barriers at the end of the Kemmel Straight.
The weekend has only one practice session, with qualifying for Sunday's race following on Friday and Saturday devoted to a standalone sprint.
The governing FIA said the practice times would not be used to set the starting grid in the event of qualifying being rained out.
It said the priority was to run a qualifying session for Sunday's race and other sessions could be cancelled or rescheduled.
If qualifying could not be held then the grid will be set by championship order.
Verstappen, winner of nine of the 11 races so far, leads the championship by 110 points but will have a five place grid penalty for exceeding his gearbox allocation.
The weather and the danger of racing in poor visibility at Spa has become a pressing concern for drivers after the death of Dutch 18-year-old Dilano van 't Hoff in a junior series race in early July.
"I think the FIA have to be bold with their decisions when it comes to safety and visibility," Mercedes driver George Russell said on Thursday.
"We all want to race but when you're going down that straight at over 200mph and you can't see 50 metres in front of you, there will be huge incidents. So they have a big responsibility this weekend."
