Injuries blunt United attack for Basel
Rooney missed Saturday's 1-1 draw with Stoke City in the Premier League after injuring his hamstring in training, while his usual strike partner Hernandez was forced off early in the match with a dead leg.
Defenders Jonny Evans and Chris Smalling will also miss the match against the Swiss side at Old Trafford with ankle and groin injuries respectively.
"He's not playing tomorrow," Ferguson said of Rooney, who has scored nine league goals this season.
"It's difficult to assess hamstring injuries... he did a bit of jogging this morning but that's all. It's difficult to say [when he will be back]."
Ferguson added at Monday's news conference that Hernandez's injury was "straightforward" and expected him to be available for Saturday's home league game against promoted Norwich City.
United drew 1-1 at Benfica in their opening Group C game in Europe's elite club competition. Basel were 2-1 winners over Romania's Otelul Galati.