Smith, who plays the timelord, won the gong for best Male Drama Performance, while Gillan, who plays his sidekick Amy Pond, picked up the female equivalent.
The pair took home the prizes for Male Drama Performance and Female Drama Performance for their roles as the Doctor and Amy Pond in the BBC One sci-fi series.
Matt beat 'Shameless' star David Threlfall, John Barrowman - who was nominated for his performance in 'Doctor Who' spin-off 'Torchwood' - and 'Doc Martin' actor Martin Clunes to the honour and paid tribute to everyone who works on the programme as he collected his statuette.