Sevilla have beaten Freiburg away from home to secure top spot in Group H.
However, the Germans are out after Slovan Liberec beat Estoril 2-0 in the other group match.
The match was only two minutes old when Pavel Krmas tested Javi Varas with a header from a free kick.
The German side were steady in the opening stages, restricting their opponents to very little, and it could have been 1-0 but again Varas did well, this time saving Admir Mehmedi's free kick.
However, Sevilla stole a lead before half time. Ivan Rakitic found Diego Perotti, who waited for Vicente Iborra to make his run before putting it on a plate for the striker.
Varas again saved from Krmas, but the home side thought they had equalised when Nicolas Hofler put the ball in, only for the goal to be ruled out for handball.
Oliver Baumann then denied Perotti as Freiburg pushed forward in search of a goal.
Sebastian Kerk put in a dangerous cross, which Varas dealt with, but the hosts were unable to match their workrate with guile.
Unai Emery's men doubled their lead in the last minute as Raul Rusescu tucked the ball home.
