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The home side held a 4-1 lead coming into the contest following last week's first leg, and they had a great chance to extend their lead with 30 minutes played.
Corentin Tolisso got on the end of a cross in the six-yard box, but his header came back off the post to keep the scores level on the night.
It looked as though the half was going to finish goalless until Bafetimbi Gomis scored in the third minute of added time, skipping past opposition defenders before driving the ball inside the left post.
Duson Uhrin's side looked to stage a comeback after scoring twice in quick succession in the second half. First, Daniel Kolar converted after being played in by Patrik Hrosovsky on the hour, before Milan Petrzela crossed for Stanislav Tecl to give the hosts the second-leg lead.
Stanislav Tecl could have made it an even more tense finish for Les Gones, but he missed from the spot with 20 minutes remaining to all but end his side's hopes.