The England international, who has scored nine Premier League goals this season, played in Saturday's 1-0 win at Swansea City.
"Wayne Rooney got a few knocks on Saturday, he missed training today, but should be OK for tomorrow," Ferguson told a news conference.
He added that defender Jonny Evans had a tight hamstring but should also be available for Tuesday's game.
United and Benfica have eight points from four matches, with the Old Trafford club ahead on goal difference.
Victory would put the winners through to the knockout stage with a game to spare. A draw would qualify both if Basel lose to Otelul Galati.
Topping the group is a priority for Ferguson, not just as it should ensure his team avoid some of the tougher prospects like Barcelona in the next round but because it would mean playing the last-16 second leg at home.
United have lost only one of their last 34 Champions League games at Old Trafford dating back to 2005.
"It's a big game, a game we recognise as a real European game in the history of Benfica and ourselves," said Ferguson referring to United's 1968 final victory over the Portuguese that won them the trophy for the first time.
"Both teams want to win so it should make it an open match."
TOUGH GAMES
The game has extra significance for United's Portugal winger Nani, who played for Benfica's bitter city rivals Sporting before his move to Old Trafford in 2007.
"I used to play against Benfica in games that used to be just like Manchester United against City - tough games," he said.
It was perhaps an unfortunate mention of City, who thrashed United 6-1 at Old Trafford last month in the Premier League, but Nani was confident he knew how to beat the Portuguese.
"Their strongest point is in midfield so if we are able to control the midfield I'm sure we have a good chance to have a positive result," he said.
"I'm sure Benfica will play some good football but with a lot of care as well, they know they are playing away."
United go into the game on the back of five successive wins with clean sheets following the City hammering and, with players now beginning to return from injury, Ferguson was hopeful of being able to field a more settled team soon.
"It doesn't disrupt us to a great degree but it does upset the balance of the team at times," he said of a recent stream of injuries.
"Sometimes we're having to think and re-think about which team we need to win a match whereas sometimes when the team is in full flow you don't need to worry about that.
"We've had a few issues which hopefully we're gradually getting over. [Defender] Chris Smalling should be back, Rafa [Rafael] is back, once we get players back we'll be OK."
