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.