Nico Rosberg pipped his championship leading team mate Lewis Hamilton, who has a 21-point lead after 10-of-19 races, by 0.242 seconds.
The German's best time of one minute 51.082 seconds around the longest track on the calendar came in bright sunshine that looked set to last despite Spa's reputation for capricious conditions. He put in the best lap despite being sidelined early on by an engine problem.
Maldonado, living up to the unfortunate 'Crashtor' moniker that has kept his mechanics busy, brought out the red flags after 50 minutes of the session when he lost control at Malmedy and smashed into the barriers.
Maldonado targets 2017 return to F1
A website chronicling the Venezuelan's unhappy status promptly changed its status from 'Nope' to 'Yes!' and reset the clock for the next update.
Behind the Mercedes drivers, Australian Daniel Ricciardo -- last year's winner for Red Bull -- was third fastest in a competitive 1:51.373 that will be a boost for beleaguered engine partners Renault.
Ferrari's Kimi Raikkonen, a four-times winner at Spa, responded to being handed a new contract for 2016 by lapping fourth fastest with four-times world champion team mate Sebastian Vettel fifth.
Belgian-born Dutch teenager Max Verstappen, the closest to a home driver the local fans have to cheer on this weekend, was seventh fastest for Toro Rosso ahead of Spanish team mate Carlos Sainz.
McLaren again struggled, despite upgrades to the Honda engine, with Fernando Alonso 16th fastest and Jenson Button languishing in 18th.
Lotus confirms Maldonado for 2016
Hungarian Grand Prix
Hamilton cruises into pole position