The England international only came on as a 73rd-minute substitute against Real Madrid in United's biggest game of the season on Tuesday when his side were 2-1 behind and reduced to 10 men after the controversial dismissal of winger Nani.
"He will be here next year, you've got my word on that," Ferguson told a news conference after British media reports had suggested Rooney could leave the club at the end of this season.
"He will be involved on Sunday [against Chelsea in their FA Cup Quarter-Final], no doubt about that.
"There is absolutely no issue between Wayne Rooney and I, to suggest we don't talk to each other on the training ground is absolute nonsense," Ferguson added.
"He understood the reason for not playing him was completely tactical and I think we were right... [Danny] Welbeck is the best player we have in terms of operating in a double role [attacking and tracking back]."
It was the first time Ferguson had addressed the media since Tuesday's match when he was too distraught to speak publicly, sending assistant Mike Phelan to the news conference instead after Nani's 56th-minute red card completely changed the game.
He arrived at the training ground smiling and asking whether reporters wanted to "do the nonsense first" or "talk sense" and was anything but the angry manager who remonstrated so furiously during the Champions League last 16 second leg match.
"It's hard to keep your faith in the game when you see what's happened in the last few years. It's the third time we've been knocked out by a referee's decision," he remarked.
"I thought it was a nice time for a chat with Jose and a nice glass of wine, relax a bit," he explained.
"I think Mike was the right one to go out, [he was] calm, very good at press, I'm going to give him more."
He had his concerns before the game over the referee as Turkey's Cuneyt Cakir had a previous history of sending off players from English teams.
"I had a big worry about it," Ferguson said before making it clear he did not want to dwell on the past.
"In the analysis in the cold [light] of the day you realise for Manchester United you just have to get on with it, nothing can be done now," the 71-year-old Scot said.
"I've cleared my mind now and just have to get on with it, this is just another day in the history of the club, it's not a good day but another day. My job now is to galvanise the troops, who were fantastic on Tuesday."
