Capaldi previously appeared in the series in an episode called The Fires of Pompeii opposite David Tennant and Catherine Tate and also played John Frobisher in Doctor Who spin-off, Torchwood.
He’s currently filming a new BBC One “contemporary take” on the classic novel The Three Musketeers in which he plays Cardinal Richelieu.
He’ll be the twelfth actor to play the part when he takes over from Matt Smith at Christmas.
The actor is known for his portrayal of the foul-mouthed spin doctor Malcolm Tucker in political satire The Thick of It.
Smith announced his departure earlier this year but has two further adventures ahead of him – the 50th Anniversary special and the now traditional Christmas special.
The anniversary special will see Smith team up with predecessor David Tennant and acting legend John Hurt, who plays a previously unknown incarnation of the Timelord.
The Doctors will be joined by companions Clara (Jenna-Louise Coleman) and Rose (Billie Piper) for a story which sees then encounter both the Daleks and Zygons.
The new Doctor Who star was announced on Sunday in a special live BBC One show hosted by Zoe Ball.
The programme included in-studio appearances by Fifth Doctor Peter Davison and Bernard Cribbins and contributions from Sixth Doctor Colin Baker and former companions including Janet Fielding and Bonnie Langford.
Executive Producer and head writer Steven Moffat said Capaldi had “briefly” occurred to him when casting Matt Smith.
In a statement Moffat said: “It’s an incendiary combination: one of the most talented actors of his generation is about to play the best part on television. Peter Capaldi is in the TARDIS!”
Ben Stephenson, Controller, BBC Drama Commissioning added : “We started thinking Peter Capaldi might be the right person to take on this iconic part a few months ago. But it was only when he did a secret audition at Steven’s house under the cover of darkness that we knew we had our man.
“He’s an extraordinarily talented actor who can seemingly turn his hand to anything. We can’t wait to premiere his unique take on the Doctor on Christmas Day and we are sure he’s going to become one of the all-time classic Doctors.”