Ferguson preferred Danny Welbeck to Rooney, 27, for the Champions League last 16 second leg at Old Trafford and Rooney only made it on to the field as a late substitute in the 2-1 defeat.
The United manager commented before the match that Rooney “needs games”
and the England striker’s omission led to questions over his United future.
Reports suggested that Rooney, who joined United from Everton in 2004, could leave as soon as this summer.
But Ferguson has moved to quash any suggestion that Rooney will be departing and insists the striker understood his reasons for selecting Welbeck to block the influence of Real Madrid’s Xabi Alonso.
He also categorically insisted that Rooney will be at Old Trafford next season and will feature in the FA Cup quarter-final against Chelsea on Sunday.
Ferguson said: “There’s absolutely no problem. He will be here next year, you have my word on that. There are no issues at all with the player. He’ll be involved on Sunday, no doubt about that.
“There’s absolutely no issue between Wayne Rooney and I. To suggest we don’t talk on the training ground is absolute nonsense and he understood the reasons for not playing him were completely tactical and I think we were right.
You don’t always get it right but I think we got it right. Welbeck is the best player we have in terms of operating in a double role.
“We had to stop Alonso’s ability to control the game which he did and it took away his control of the match and ability to go further forward and be an attacking player.
“You don’t always get it right but we definitely did on Tuesday.”
United led through a Sergio Ramos own-goal on Tuesday night but after Turkish referee Cuneyt Cakir sent Nani off for a challenge on Alvaro Arbeloa, Real hit back through Luka Modric and Cristiano Ronaldo to progress.
Ferguson was too angry to attend the post-match media conference.
The United manager was furious with the official at the time but insists United must move on.
The United manager added: “On the issue of the referee quite simply it’s hard to keep your faith in the game, when we see what’s happened in the last few years.
“It’s the third time we’ve been knocked out (of the Champions League) by of a referee’s decision. It’s not easy to take but in the cold analysis of the day, you realise we’re Manchester United and we just have to get on with it.
“Nothing can be done now and the important issue is the quarter-final on Sunday. It’s clear in my mind now and we have to get on with it.
“It’s another day in the history of our club. Not a good day but another day. My job now is to galvanise the troops who were fantastic on Tuesday and we owe the support a good performance on Sunday.”
Asked if he had concerns about Cakir before the match, Ferguson said:
“I was definitely concerned, I said that to the staff but it’s gone.
There’s nothing we can do about it.”
The United manager sent his assistant, Mike Phelan, to attend Tuesday’s press conference and will use his number two for media duties on a more regular basis.
He said: “Mick was the right one to go out. He’s calm, he’s very good with the press and I’m going to use him more. That was a nice time to have a chat with Jose (Mourinho) have a nice glass of wine and relax a bit.”
Utility man Phil Jones is set to miss Sunday’s game with an ankle problem that kept him out against Real Madrid.