Rooney missed United's 1-1 Premier League draw against Stoke City at the Britannia Stadium on Saturday, Mexican international Hernandez also missed most of the game after coming off with a leg injury.
Dimitar Berbatov and Michael Owen are expected to start up front on Tuesday.
Speaking about Rooney, Ferguson admitted that he could not say when the player would be back in action, but he will definitely miss out against Basel.
Ferguson told reporters: 'He's not playing tomorrow. It's difficult to assess with hamstrings but we hope we have him back quickly. He did a bit of jogging this morning but that's all.'