The 20-year-old was forced off in the first half at Old Trafford and ended up leaving the stadium on crutches after goals from Nani and Javier Hernandez secured United passage to the quarter-finals.
Ferguson has ruled Jones out of this weekend's clash with Queens Park Rangers and said that scans will indicate whether he will be fit for the return leg against Ronaldo's Real Madrid on March 5.
"We'll have to assess it in the morning," said Ferguson. "It's an ankle injury obviously so I'd imagine he'll not be ready for Saturday anyway.
"But we'll see what he's like after that."
Jones missed the first three months of United's season with a leg injury.