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.
Portugal winger Nani was sent off after a high-footed collision with Real defender Alvaro Arbeloa with United leading 1-0 at the time.
The Spanish visitors scored twice in the next 13 minutes through Luka Modric and Cristiano Ronaldo to go through to the quarter-finals 3-2 on aggregate after a 2-1 win on the night.
Even Real coach Jose Mourinho questioned whether Nani should have been dismissed, saying on another occasion it could have been a yellow card. Ferguson was still stunned by the sending off.
"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.
Ferguson also said he had made the right call in letting his assistant do the talking in the aftermath of the defeat, regardless of the fact the club faces UEFA disciplinary proceedings for failing to fulfil their media obligations.
"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.
His focus now is firmly on the two remaining chances of silverware in the shape of the FA Cup and the Premier League, where they hold a 12-point lead over champions Manchester City.
"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."
United will face Chelsea without defender-midfielder Phil Jones, who is still out with an ankle injury but should be available next week.
Midfielder Ryan Giggs, who played the full game against Real in which he reached 1,000 professional appearances, will a
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