Red Bull's Mark Webber posted the fastest time before heavy rain returned to mar the second practice for the Belgian Grand Prix on Friday.
The Australian clocked 1 minute, 50.321 seconds, with Ferrari's Fernando Alonso second quickest in 1:50.461, and McLaren's Jenson Button third in 1:50.770.
Heavy rain affected the morning's first practice, and, although the conditions were much improved, another big downpour arrived nearly one hour into the second session.
Defending F1 champion Sebastian Vettel was only 10th fastest, but took no risks in the treacherous conditions.
Webber, who is still seeking his first GP win 11 races into the season, went out again briefly toward the end of the session but kept his speed down on the soaked track.
The 7-kilometer (4.3-mile) Spa circuit is the longest and one of the most demanding on the calendar beside Monaco's track. Its famed corners, such as Eau Rouge and Blanchimont push drivers to the limit, and this prompted some cautious driving in both sessions.
Seven-time former champion Michael Schumacher was 11th fastest the second time around after posting the best time in the first practice ahead of his Mercedes teammate Nico Rosberg, followed by Button and Vettel.
Schumacher, who made his debut at Spa 20 years ago and has won the race six times, went out early when the track was still dry and before the rain starting lashing down to clock a leading time of 1:54.355 seconds.
There was a lull for some 20 minutes as the downpour was so heavy that most drivers - including Vettel, Button and his McLaren teammate Lewis Hamilton - preferred to wait for it to abate.
Vettel was followed by Hamilton, with both trailing Schumacher by more than nine seconds, although the times were of little consequence given the poor racing conditions faced by the drivers who started later.
Vettel tried to go out early on intermediate tires as his team warned him over the radio to be careful as there were "lots of rivers" on the track.
Former F1 champion Hamilton then went out for a brief run but, like Vettel, quickly came back into the pits after his car started slipping and sliding on the Blanchimont turn.
Other drivers experienced greater difficulties.
Brazilian driver Bruno Senna, making his F1 return with Renault as a replacement for Nick Heidfeld, had a miserable run that ended when he crashed into the barriers on the ninth turn. He was unhurt and his car was taken away.
Rookie driver Paul di Resta's Force India was also lifted away late in the session, after he slid sideways and slammed into the crash barriers on the same turn as Senna, prompting race director Charlie Whiting to go and inspect the turn.