Doctor Who: Shada was a run of episodes meant to mark the end of the 17th series, but the studio scenes were never completed.
The actor, 83, has returned to film part of the 1979 story, which was abandoned because of a strike by electricians.
The new scene sees Baker at the console of the Tardis in his famously long coat and stripy scarf.
Filmed at BBC Television Centre earlier this year, it combines original live-action footage with new animation as well as Baker’s cameo.
Baker was the Fourth Doctor and his appearance is his first in the role in 36 years.
In the new scene, he voices words from Douglas Adams’s original script and wonders aloud: “I expect that sometime in the future – in about 200 years’ time – someone will meet me and say is that really the Doctor? He seemed such a nice old man.”
Of the cameo, the actor said: “Shada was one of my favourite Doctor Who stories. I have many fond memories of shooting the location scenes in Cambridge, and it was disappointing not to finish the story in the studio.”
He said: “When I was doing Doctor Who it was the realisation of all my childhood fantasies … so I took to it like a duck to water and I still do.
“I loved doing Doctor Who because it was life to me…. My real life was really rather drab… I used to dread the end of rehearsal…”
Baker added: “I never left (Doctor Who) and that’s why I can’t stay away from it.”
The star played the Doctor between 1974 and 1981 and has not appeared in the role since, aside from a brief cameo as part of Children in Need.
Doctor Who: Shada is being released as a digital download now, and on DVD and Blu-Ray on Monday December 4.
