Rooney confirmed his intention to quit Old Trafford in a statement on Wednesday night, claiming a lack of investment in the first-team squad was the prime reason for his decision.
Ferguson has dismissed a suggestion that he might suspend the 24-year-old, who missed the 1-0 Champions League home win over Bursaspor with an ankle injury.
But Rooney's comments have created a stir the United boss is anxious to sort out.
"We don't want it to become a saga. We have the team to consider," he said.
"We will put it to bed tomorrow.
"I have not read all the statement but we will consider it tomorrow.
"David Gill and I have a meeting at 10am tomorrow morning. David has spoken to the owners tonight, which is important.
"It is really important for us to put it to bed.
"I am manager of a club that is trying to win a game on Sunday against Stoke City.
"That is the most important thing. The rest is a bagatelle."
Ferguson did show signs of being rattled by four days of intense debate around Rooney's career, which first erupted on Sunday morning.
"I am not going on with this all night. Stop it now," he said.
"It is a European game. You have had plenty yesterday. There has been plenty tonight. I am concentrating on the game. Failing that, forget it."
Asked about the possibility of suspending Rooney, he replied: "What kind of imagination have you got?"
Nevertheless, there must be the prospect of some kind of sanction following the devastating assessment of United's future provided by their number one player, who may never pull on a red shirt again such is the furore his comments have caused.
And Ferguson is clearly not convinced Rooney is making the right decision.
"Sometimes you look in a field and see a cow," he said.
"You think it is a better cow than the one you see in your field. It never really works out that way.
"Some players like to think the world is better somewhere else. It never really works."
So many questions have been asked of United's fortunes that Ferguson himself could be forgiven for having doubts.
After watching his side triumph thanks to Nani's sixth-minute effort, Ferguson insists he has none.
"To maintain the success at any club is not a certainty," he said.
"I always believe a four-year cycle is the most you can achieve. Very few teams can go beyond that.
"Last season we almost did it. We were one point short of winning the league.
"But we realised some time ago that Ryan Giggs, Paul Scholes and Gary Neville were not going to last forever. Therefore our policy is to develop footballers in the place."
He then recounted a story from United's last period of relative decline after 2004, which involved Rooney himself, and included the departures of star names Roy Keane and Ruud van Nistelrooy.
"A player said to me Wayne Rooney and Cristiano Ronaldo were not good enough and he wasn't prepared to wait," said Ferguson.
"That is the problem with potential. People don't identify potential. We are very good at it. I have identified it all my life. I know potential. I know where it can be developed and how to develop it. I have faith in it.
"That is what this club is about. When you see Manchester United at the moment, with 14 players under 22, you don't see the Manchester United for years ahead.
"We will invest in signature players when the time is ready. We were not ready this summer."
Apart from one exception, which is thought to be David Villa, who left Valencia for Barcelona.
"There was one player we would have liked to get, but he chose another club," said Ferguson.
"Some players don't want to leave their country.
"But Manchester United is a big attraction for any player.
"In terms of the future of Manchester United, there are a lot of things in my favour.
"If I told you how many agents phoned me in a week, saying a player would love to play for us - and I am not just talking about run-of-the-mill players - it would amaze you.
"We still have that fantastic romance, and respect from everyone.
"But we will be OK. I have every confidence. The structure of the club is good. We have the right staff, the right manager, a brilliant chief executive. There is not a thing wrong with Manchester United.
"We will carry on."
It all rather overshadowed Bursaspor coach Ertugrul Saglam.
"We wanted to perform to the best of our ability but I don't think we played very well," he said.
"I don't believe United played as well as they would have liked either, so it has not been a very eventful evening."
Maybe not on the pitch. Off it is a quite different story.