Fabio was making his United debut when he injured his calf early in the second half, while fellow 18-year-old Welbeck limped out of the tie late on with an ankle problem.
"Danny Welbeck got kicked on the ankle. It's nothing serious but I don't think he'll make Tuesday," added Ferguson.
"Young Fabio has a calf strain and it's disappointing because he's only just come back from a long injury. He did very well too."
They join fellow defenders Wes Brown, Rio Ferdinand, Patrice Evra and Fabio's twin brother Rafael on the sidelines for the Premier League leaders.
Anderson, Nani, Wayne Rooney, Wes Brown, Jonny Evans and Ji-sung Park were also unavailable for Saturday's game.
Cristiano Ronaldo was withdrawn after 71 minutes against Spurs and after the game Ferguson admitted the Portuguese winger was a doubt prior to the match.
"We had to get the doctor in to see Cristiano," said the Scot.
"He had a bit of a bug and I think it showed today, I don't think he was anywhere near ready.
"But he showed the appetite to play and it's always good to have him on the pitch, opponents are always aware of him. He should be better by Tuesday."
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