Stuart Campbell, editor of Wings Over Scotland, claimed he had been victim of censorship after his channel on the video sharing website was abruptly suspended last weekend.
Mr Campbell had shared dozens of videos, many of which contained clips from BBC current affairs programmes, in recent years.
The channel was restored to YouTube this morning, but without 13 videos at the centre of the dispute. The BBC had claimed the 13 videos shared on the channel breached its copyright.
The broadcaster now has two weeks to appeal against the decision through the courts. If no appeal is lodged, the 13 videos will also be allowed to return to the Wings Over Scotland channel.
A spokesman for the BBC said it regularly took action to protect its copyright “whenever we receive complaints about large volumes of our material being posted or used without authorisation”.
Ian Small, BBC Scotland’s head of public affairs, said there was no editorial control over such decisions as they centred on purely copyright issues.
Mr Campbell told The Scotsman: “I hope that the BBC representative’s comments on the John Beattie show today signal that this outbreak of insanity is now over and we can get back to scrutinising Scottish politics and holding politicians to account.”