The England striker was dropped by Ferguson for Tuesday's round of 16 tie second leg against Real Madrid, with Danny Welbeck preferred.
"He'll be here next year," Ferguson said. "You can have my word on that."
Ferguson was also speaking for the first time about Nani's controversial sending off in the 3-2 aggregate loss to Madrid. "This is the third time we've been knocked out by the referee's decision, it's not easy to take," he said.
Ferguson said: "There is no issue between myself and Wayne Rooney. To suggest we don't talk is nonsense.
"He understood the reasons completely. Tactically we got it right. We don't always but we did then.
"Welbeck is the best player we have in terms of operating a double role. We had to chalk out Xabi Alonso's ability to control the game, which he did, and also his ability to go further forward as an attacking player.
"I left out Shinji Kagawa after he scored a hat-trick. I thought I would get more stick for that."
Ferguson, who revealed he had banned The Daily Mail and The Independent newspapers "until they apologise" for the Rooney story, said the striker would be involved against Chelsea in the FA Cup quarter-final on Sunday.
However, he declined to say if he would start.
"Why should I help anyone by telling them my team? We don't do that," Ferguson said. "But Wayne does need a lot of football. He has always been that type."