Rooney was part of the United side that beat Swansea 1-0 at the Liberty Stadium on Saturday but suffered a knock in a collision with goalkeeper Michel Vorm and was rested while the rest of the squad were put through their paces at the club's Carrington complex on Monday.
But the England striker is still expected to feature against Portuguese side Benfica, with the Red Devils needing a win to top Group C.
"Wayne Rooney got a few knocks on Saturday, he missed training today, but he should be OK for tomorrow," Ferguson said in his pre-match press conference.
The United boss also said he expected centre-back Jonny Evans to be available despite a tight hamstring, although fellow defender Chris Smalling is out with a foot injury and striker Danny Welbeck remains doubtful with a muscle strain.
United and Benfica lead the group with eight points, with United ahead on goal difference. Victory for either on Tuesday would put them through to the knockout stage as group winners with a game to spare. A draw would send both through if Basel lose to Otelul Galati.