It comes after Darren 'Birdie' Bird's image - showing the mascot "paying his respects" to Sir Terry, who died on Sunday - was shared thousands of times on social media.
Pudsey has a tear running down his face and his colourful eye patch is black.
Mr Bird, aka Birdie, said: "Little did I know it would go as big as it did."
His tweet has been shared more than 3,000 times and the image now appears on Children in Need's profile picture on Twitter and Facebook, where it has been liked by more than 50,000 people.
"It's an absolute honour - to feel that it spoke to them and that they see it as a perfect tribute to Sir Terry," said Mr Bird, who is from Ipswich.
"As a cartoonist it's such a sad way to have your artwork shared, but equally to have the reaction and to have Children in Need embrace it in such a way is just really lovely."
Mr Bird, whose work has appeared in the Racing Post and on Channel 4, said he had admired Sir Terry for being a "quick-witted" entertainer who "brought a lot of light into people's lives".
A cartoonist's tribute to Sir Terry Wogan showing Pudsey Bear in mourning has been adopted by the official Children in Need charity.