Former France international Rougerie, who has played 44 matches and scored 17 tries in the competition, including two this season, was left out of the squad for Saturday's match with a thigh problem, the Top 14 leaders said.
Back row Gerhard Vosloo has a similar injury and will also miss the tie to be played at Montpellier.
However, Clermont Auvergne's bid for a first Heineken Cup final received a boost when Australian James was given the green light after recovering from a thigh injury that sidelined him for a month.
"Morgan Parra and Brock James will form the usual final stages' halves pair," the club said.
- Sports & Recreation
- Gerhard Vosloo
- Clermont Auvergne