The England striker missed training on Monday morning, raising fears that he could be absent for Tuesday's night's key Group C clash at Old Trafford.
Ferguson told Sky Sports News: "Wayne Rooney got a few knocks and missed training today, but he should be OK for tomorrow.
"We've got one or two knocks from Saturday. Jonny Evans got a little tightness in his hamstring yesterday, but hopefully will be OK for tomorrow.
"Chris Smalling trained today but won't be available for tomorrow, but he should be OK for Saturday."