Wayne Rooney missed Saturday's 1-1 draw at Stoke City with a hamstring problem and will not return until next weekend's Norwich City game at the earliest.
Ferguson will also be without Javier Hernandez, who sustained a dead leg at Stoke, Chris Smalling, Jonny Evans, Nemanja Vidic, Rafael and Tom Cleverley for Tuesday's game.
That means he will probably have to use Antonio Valencia at right-back, while Dimitar Berbatov, Danny Welbeck, Michael Owen, Federico Macheda and Mame Biram Diouf will compete for the right to start in attack.
Basel top Group C after beating Otelul Galati but Ferguson says that his squad has sufficient depth to cope with the Swiss champions despite all their absentees.
The United manager would not be drawn on whether Berbatov will start but insists his players are used to being rotated.
The Bulgarian was left out of the squad for last season's Champions League final and has started just two games this season.
But Ferguson said: "They understand that having the squad gives them a better chance of winning things.
"They accepted the squad system a long time ago and want to do well when they get the opportunity because as a group they all want to do well, so I don't have any issues with that at all.
"Of course Dimitar still has a big part to play. He's one of our squad members and they all have a part to play.
"With the Premier League, the Champions League, the Carling Cup, the FA Cup -- it's an exhausting season unless you use your squad.
"I don't need to reassure him, he knows he's a part of the squad. It applies to other people in the squad -- Macheda, Diouf, Owen.
"We've had six games, one game at Benfica, one game at Leeds, it's only early doors. There's still plenty of time."
Despite reaching three finals in the past four seasons, Ferguson rejects suggestions that his team are enjoying a 'golden period' in the Champions League.
The United manager, who has won the tournament twice, feels his team should have won the trophy more often over the past two decades.
"I think that Champions League is the best competition in the world now; better than the World Cup, better than the European Championship. It's fantastic entertainment.
"It's not a golden period because we lost two finals so you wouldn't call it a golden period.
"But we've been consistent in the Champions League. Our form away from home has been outstanding.
"We hope we can do better this year and win it because that's the aim of this club all the time.
"Basel have good experience, they've been in Europe quite a few times and we'll respect that."
Ashley Young, who joined from Aston Villa in a £20 million deal ($31m) in the summer, is hoping to make his Champions League debut.
The England winger, 26, has impressed in his early weeks with United despite admitting the change has been a major upheaval.
He said: "I'm very excited. Coming to a club like United to play in competitions like this is any boy's dream and I hope to be selected and play a part.
"We know it will be a tough game but we'll will look to impose ourselves like we have in every game this season and hopefully that will bring three points.
"When we went on the pre-season tour I noticed how big the club was and you can see the difference with the size and the quality of the squad.
"When you come to a club like United, you know it will be a challenge and I always wanted to challenge myself at the top level.
"There's always competition at a club like United and you've got to be on your toes 24-7 or someone will take your spot."
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