He was the only driver to go quicker than the one minute 43 second mark.
Vettel, hoping to end his victory drought that goes back to last year’s Belgian race, was hindered by traffic on his fastest lap and ended up 0.748 seconds adrift.
He was very nearly beaten by Lewis Hamilton who took third. The Briton, who leads the overall standings by 62 points from team mate Valtteri Bottas, had crashed in Saturday’s final practice session. His Mercedes mechanics worked a miracle to repair his car in time for qualifying.
Saturday's pole was the third of Leclerc’s career. The 21-year-old, in his first season with Ferrari and only his second in Formula One, had looked favourite to seize it after topping the first two phases of qualifying building up to the pole-position shootout.
But, having been denied his first win of the season by an engine problem in Bahrain where he also started from pole, he isn't taking anything for granted, even with Ferrari’s speed advantage around the fast sweeps and flat out blasts of Spa.
Behind the top three, Bottas will line up alongside team mate Hamilton in fourth, with the two Mercedes cars nearly touching as the field bunched up on their warm up laps. Max Verstappen, enjoying plenty of support from his orange-clad Dutch fans, was fifth.
Daniel Ricciardo, carrying an engine-related penalty that will drop him down the grid, was sixth ahead of Renault team mate Nico Hulkenberg, who is also carrying a grid penalty. Kimi Raikkonen was eighth for Alfa Romeo ahead of Racing Point driver Sergio Perez.
Kevin Magnussen rounded out the top ten for the Haas team. Robert Kubica was the first casualty of the session when the Mercedes engine in his Williams let go spectacularly, belching smoke and flames.
The German manufacturer has brought an upgraded power unit this weekend. But questions have been raised about its reliability with Perez, whose Racing Point also has a Mercedes engine, suffering a failure during Friday’s practice. Alfa Romeo’s Antonio Giovinazzi also ground to a halt, with both incidents briefly halting the session under red flag conditions.