The Scottish actor starred as the 10th Doctor with Piper as his sidekick Rose Tyler, and both will return for a one-off episode alongside current Time Lord Matt Smith and his new assistant played by Jenna-Louise Coleman.
Executives at the BBC, which airs the show in the U.K., also confirmed Harry Potter star John Hurt will be joining the cast of the special 3D episode, which will air in Britain on November 23.
In January, Piper denied she would be taking part in the anniversary show, telling U.K. TV host Graham Norton, "I wasn't asked, no. I think Matt Smith may have said, in passing or in jest, it would be nice (for me to be involved).
"I think maybe he said that and then it became something quite different (a rumor), but no."