With new signing Robin van Persie handed a full debut, Rooney was only amongst the substitutes as Shinji Kagawa was also named in Ferguson's starting line-up.
It was a major call by the United boss following Rooney's below-par display in the defeat to former club Everton on Monday.
Brazil full-back Rafael returns to bring some solidity to a defence which again features Michael Carrick in the centre, with Jonny Evans on the bench.
However, it was the absence of Rooney that was the major talking point.
When Ferguson left the striker out for the home game against Blackburn on New Years Eve as a disciplinary measure, United lost, a defeat that proved costly in the Premier League title battle.
No immediate explanation has been offered for Rooney's omission.
But when United fans welcomed Van Persie's arrival last week, it was in anticipation of last season's Golden Boot winner playing with Rooney rather than instead of the 26-year-old, who scored 35 goals in all competitions for the Red Devils last term.