In a wet and eventful session, the 24-year-old German secured Red Bull's 13th pole in a row and his ninth of the season.
Vettel's Australian team-mate Mark Webber, celebrating his 35th birthday with a new one-year contract, will line up third and alongside Ferrari's Brazilian Felipe Massa.
Seven-times world champion Michael Schumacher, who made his debut at the circuit 20 years ago, had a nightmare afternoon and failed to set a time in the first phase after skidding his Mercedes into the wall.
Hamilton, winner at Spa last year, found himself in the middle of another controversy after clashing with Williams' Venezuelan Pastor Maldonado in the second phase of qualifying.
The Briton forced his way past Maldonado as the seconds ran out and then, after completing the final lap, appeared to be cut up by the Venezuelan with the McLaren damaged by the contact.
"It was done deliberately," Hamilton said over the team radio of the rookie's actions. McLaren fitted a new front wing and patched up the car for the final phase.
There was no immediate comment from race stewards but Hamilton said he was expecting the call, with both drivers facing possible sanctions.
The two men had also clashed at Monaco earlier in the year, with Hamilton tipping Maldonado into the tyre barriers when the Venezuelan was heading for his first points finish.
Hamilton's team-mate Jenson Button, winner in Hungary before the summer break, was left in 13th place on the grid after a 'misunderstanding'.
The 2009 champion was told to pit, an order he questioned by saying "Are you sure? Are you sure?", during the second session and then had to watch as his time proved too slow to make the cut.
Schumacher's hopes of a first podium since his comeback last season suffered a major setback with the 42-year-old facing a back-row start.
The German skidded on a wet patch before he could set a timed lap, crashing into the wall as a rear wheel came off the Mercedes and rolled down the track.
Brazilian Bruno Senna made an impressive start to his first race weekend with Renault, qualifying seventh and ahead of Ferrari's Fernando Alonso in eighth place.
Senna's Russian team-mate Vitaly Petrov qualified 10th.
Meanwhile, Force India’s chance of scoring some points look bleak as Adrian Sutil will start the race from 15th position while his team-mate Paul di Resta from the 18th spot on the grid.
Di Resta could not even enter the Q2 as his best effort in Q1 was 2:07.758 from eight laps. The Scott could have taken a better position but his car spun near the end of the session after being bumped by Heikki Kovalainen of Lotus.
Belgian GP qualifying
