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.