Rooney was a doubt after missing Saturday's 1-0 Premier League win at Wolverhampton Wanderers with a knee injury picked up on England duty but he will feature at Old Trafford.
Ferguson feels his return is a major boost as they plot a course to the quarter-finals and said the England forward's availability was not something he could take for granted.
"It was a worry. His injury prevented him playing on Saturday and on Friday I didn't think he had any chance but he's progressing. He has made a rapid improvement from Saturday," Ferguson told a news conference ahead of the last 16 game.
Rooney, who has scored 23 Premier League goals this season, proved his fitness after coming through training on Tuesday.
United, who won the first leg of the first knockout round tie 3-2 in the San Siro, are without England defender Wes Brown who could be sidelined for up to six weeks after scans revealed he broke a bone in his foot during the victory over Wolves.
"Unfortunately, his career has been blighted with injury. He has got another one and will be out for four to six weeks but I hope I can get him back for some of the season," Ferguson added.
United will also be missing suspended midfielder Michael Carrick and injured duo Michael Owen and Ryan Giggs.
FERGUSON OPTIMISTIC
Ferguson's team were knocked out at the semi-final stage by Milan in 2007 and the Italians also progressed from the first knockout stage at United's expense in 2005.
But Ferguson is full of optimism ahead of the game with Leonardo's side despite Clarence Seedorf's late strike cutting their advantage to just one goal in the first leg.
"I can understand that Milan are fairly confident after getting that second goal. It will give them encouragement. If they hadn't got that it would have been very difficult for them.
"Three years ago they beat us well but the preparation was completely different. Physically we weren't ready for that kind of match.
"They'd rested players on the Saturday. It's a completely different scenario. My team has got to produce and they will produce," he added.
"Historically, they are one of the best teams of all time in Europe and it was a landmark victory for us in Milan."
