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-time 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 tire barriers when the Venezuelan was heading for his first points finish.
Hamilton’s teammate 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.
“That is massively disappointing and a huge shock,” he said. “A big mistake on our part. In every practice session we’ve been in top three. Tough being back in 13th but we’ve got to deal with it.”
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.
“I don’t know what happened,” he said over the team radio after the car came to a halt. “It’s something unexpected.”
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 teammate Vitaly Petrov qualified 10th.
Force India’s British rookie Paul di Resta was another casualty of the first session after spinning on his flying lap.
Both the HRTs and Virgin Racing’s Belgian Jerome d’Ambrosio were at the mercy of the stewards after failing to meet the 107 percent qualifying threshold, along with Schumacher.
The second phase of qualifying was halted briefly after Force India’s Adrian Sutil spun and skidded into the tire wall at the top of Eau Rouge.
