Rooney returned from international duty with a groin injury, while Rafael suffered a similar problem during Saturday's win at Sunderland.
"Wayne and Rafael started training this morning, which is good news. They should be fine by Monday," Ferguson said.
Ferguson is also hopeful skipper Nemanja Vidic and Jonny Evans will have recovered from back and hamstring injuries respectively.
"They are not there yet, but we have time on our hands to get them right," he said.
One player who definitely will be involved is Robin van Persie, even though his barren spell in front of goal for United extended to nine games with failures at Sunderland - when the winner was credited to Titus Bramble - and Chelsea.
"Robin doesn't need a rest that's for sure," said Ferguson.
"He is a strong lad with a great physique.
"It's disappointing that he wasn't awarded the goal at Sunderland, I can understand that because it took a wicked deflection, because the shot was fantastic.
"All strikers have little dry spells - you always hope it ends quickly. It is just part of being a striker."