The clipsaw Tennant once again as the Time Lord accidentally crashing his Tardis at the "genesis of the Daleks" - the long-standing enemy of the Doctor.
Scottish actor Tennant, who first stepped into the Tardis as the 10th Doctor in 2005, is starring as the 14th Doctor for three anniversary specials later this year.
Children in Need aired on BBC One on Friday and this year raised Â£33.5m.
Tennant revived his role as Doctorat the conclusion of the show's BBC centenary special last year,bringing an end to Jodie Whittaker's reign as the time-travelling hero.
During a new short clip played midway through the televised appeal on Friday, actor Mawaan Rizwan is seen brainstorming a name for the newly-created Dalek before Tennant crashes into and breaks it with his Tardis.
Tennant said: "Hello, just passing by because I got a bit lost - it's funny, 60 minutes ago I was this really brilliant woman and now I've got this old face back again. I mean, why?
"Oh, I'm sorry, I am so, so sorry, I think I broke this multi-clawed adaptable ... oh, that's a Dalek."
Rizwan responds: "Good word, Dalek. Yes, that's it."
"I'm lucky, I wasn't exterminated" Tennant said. "Wait, do you mean this is the genesis of the Daleks?"
After breaking the Dalek, the Doctor hands a plunger from his Tardis which marks the "origins of the iconic Dalek arm", the Doctor Who official Twitter page said.
The clip was created by Russell T Davies, who relaunched the TV series in 2005 following a 16-year hiatus.
Tennant is reuniting with Catherine Tate for a trio of 60th anniversary Doctor Who specials this year, before Ncuti Gatwa takes over the role as the 15th Doctor.
Much like James Bond, the Doctor Who role is passed on from actor to actor, thus continuing the franchise. At the end of an actor's tenure as the Doctor, the character "regenerates" with somebody else then taking on the extra-terrestrial role.
This year's televised Children in Need appeal opened with a message from Catherine, Princess of Wales.
The princess said nurturing every child was "vital" when describing why projects supported by Children in Need "are so important."
"They help the very youngest, most vulnerable members of our society feel safe, secure and loved in these important, formative years, so that they can enjoy their childhoods now, and grow to reach their potential and thrive in the world in later life," she said.
The live show also featured an appearance from BBC Radio 2 presenter Vernon Kay, whothis week completed an 116-mile ultra-marathon.
He was left speechless after it was announced he had raised more than Â£5m for the charity.
There has also been a performance from Little Mix star Leigh-Anne Pinnock and a visit to Graham Norton's notorious Big Red Chair.
The programme was hosted by Ade Adepitan, Mel Giedroyc, Jason Manford, Chris Ramsey, Alex Scott and Lenny Rush - who at the age of 14 became the first-ever child presenter of the live show.
Children in Need, which helps improve the lives of disadvantaged children and young people around the UK, has raised more than Â£1bn for charities and projects since its first major appeal in 1980.
David Tennant has returned as Doctor Who for a Children in Need sketch.