The programme also saw a surprise cameo return for Tom Baker, who bowed out as the fourth Doctor in 1981, among other incarnations of the Time Lord.
The 75-minute show had been under a veil of secrecy for months and was the climax of weeks of celebrations on TV, radio and with a huge fan convention in east London.
Last night's episode of the BBC1 programme saw The Doctor rewrite history by avoiding the annihilation of his planet Gallifrey, and instead freezing it in time and dispatching it to an unknown place in the universe.
Capaldi - who was announced as the next face of The Doctor - was glimpsed only fleetingly as his eyes looked towards the camera.
Many of the other Doctors were seen in archive footage, with CGI used to bring them together in a line-up at the show's climax.
The programme brought together current Doctor Matt Smith and his predecessor David Tennant, along with a previously barely seen regeneration played by John Hurt. The trio teamed up to avert the destruction of Gallifrey.
There were numerous nods to the past for fans from the start, with the programme beginning with the original credit sequence used in the first ever edition in 1963.
The Doctor's assistant Clara, played by Jenna-Louise Coleman, was seen teaching at Coal Hill School, which featured in the very first story, An Unearthly Child, and was attended by The Doctor's granddaughter Susan.
There was also a character, Osgood, wearing a Tom Baker-esque multicoloured scarf.
A favourite foe, the Zygons, were brought back for the occasion by the sci-fi show's executive producer Steven Moffat.
They have been seen only once before, in the mid 1970s, and in the milestone show - broadcast 50 years to the day since the programme made its debut - they adopted the form of Queen Elizabeth I.
The programme was broadcast simultaneously in 94 countries, with hundreds of cinemas around the UK also screening it with many in 3D.