Rooney, 31, has missed the last four United games with a minor leg injury and does not make the trip despite training on Tuesday morning.
Timothy Fosu-Mensah is included in the 20-man squad but full-backs Luke Shaw and Matteo Darmian miss out.
Jose Mourinho's side have a 3-0 advantage after the first leg.
Midfielder Ander Herrera is suspended and defender Phil Jones is absent with a hamstring injury.
Following the trip to France in the Europa League, United will face Southampton on Sunday in the EFL Cup final at Wembley Stadium.
Striker Wayne Rooney has been left out of Manchester United's squad for Wednesday's Europa League last-32 second-leg tie against Saint-Etienne.