Los Che lost 2-1 on the night, but progress 4-3 on aggregate thanks to Alvaro Negredo’s crucial goal. Andrea Raggi and Elderson Echiejile had scored for the French side.
Valencia will now join defending champions Barcelona, Real Madrid, Sevilla and Atletico Madrid in Thursday’s group stage draw.
It is the first season when one country having five teams in the group stages is possible after UEFA introduced an extra slot for the Europa League winners, Sevilla.
Elsewhere, Scottish side Celtic crashed out of the group stages after a 2-0 loss to Malmo meant a 4-3 aggregate loss – Markus Rosenberg and a Dedryck Boyata own-goal proved the difference.