Red Bull's triple champion lapped the 7.004 km circuit, the longest and second fastest on the calendar, with a best time of one minute 48.327 seconds set in the last two minutes of the dry session on the medium tyre.
Alonso had been quickest until then with a time 0.105 slower.
The Spaniard and Vettel, the championship leader, were quickest in Friday's first and second practice sessions respectively.
They were also at the centre of a flurry of concern about the Pirelli tyres when both suffered right rear punctures within seconds of each other in Friday's final practice.
After a full investigation, Pirelli ruled out any tyre-related issues and placed the blame on a metal plate shed from another car and found on the track during a later inspection.
There were no visible tyre problems in Saturday's session.
Australian Mark Webber, Vettel's team mate, was third fastest as he limbered up for what will be his last Belgian Grand Prix before moving to sportscar racing with Porsche at the end of the year.
Toro Rosso's Jean-Eric Vergne was fourth with Ferrari's Felipe Massa fifth.
McLaren's Jenson Button, last year's winner from pole, was an encouraging sixth on the timesheets.
Mercedes appeared to be struggling, however, with Lewis Hamilton, who will be chasing his fourth successive pole later, only 12th fastest with team mate Nico Rosberg ninth.
The timings meant Hamilton, the 2008 world champion and winner of the previous race in Hungary last month, had failed to appear in the top 10 in any of the three practice sessions.
Vettel leads Kimi Raikkonen by 38 points with nine of the 19 races remaining. Alonso is a point behind Raikkonen and Hamilton a further nine adrift.
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