Rooney was left out of United's squad by Ferguson, who feared the 24-year-old would get plenty of abuse from fans of his former club after a week of lurid allegations about his private life.
The England international and his wife Coleen issued a statement last night asking for privacy and Ferguson felt it was better for him not to be on Merseyside.
The United boss refused to comment on the situation after Everton scored twice in stoppage time to snatch a point Goodison Park, but when asked whether his missing players would be back on Tuesday he said: "They will all be available.''
At his pre-match press conference on Friday Ferguson refused to discuss the 24-year-old's situation. "Let's put it to bed straight away. I am not discussing any of my players' personal lives,'' he said.
He did confirm, in a television interview prior to kick-off, his thinking behind leaving Rooney at home. "We made a decision simply because he gets terrible abuse here. We don't want to subject him to that,'' Ferguson told Sky Sports.
In the past, Ferguson has not been afraid to leave out his big names for a variety of reasons, famously dropping David Beckham after growing tired of his off-field lifestyle, and having to deal with the outspoken criticism from within of former captain Roy Keane.
The Rooneys' statement on Friday night appealed for privacy at a difficult time for them. "The last six days have been extremely painful for us and for our families,'' the couple said in a statement. They added that it was impossible for them "to attempt to resolve any issues in the current media glare."