The Serbian defender's future has been the subject of intense speculation, with some reports linking him with a move to Spanish giants Real Madrid.
"There was a lot of speculation about Nemanja's future," United chief executive David Gill said on the club's official website.
"In my view it's been the media drumming some old stories because they certainly didn't come out of the Manchester United camp and I'm confident they didn't come out of Nemanja's camp.
"We sat down with Nemanja and his advisor at the end of last season and started discussions.
"I'm very pleased to confirm that we agreed terms with Nemanja three or four weeks ago on a new long-term deal with the club."
Gill said that Vidic, who was a member of Serbia's squad for the World Cup, is expected to pen the new deal when he returns from holiday in early August.