Dortmund - who exited their domestic Cup to third division Offenbach in October - needed to win to progress and deny their opponents a place in the last 32 but it was Sevilla who gained a much needed morale boost to end a run of five successive defeats, including three at home.
Egyptian star Mohamed Zidan had to watch the game from the stands even though he was declared fit and available for selection during the final training session.
French title contenders Paris Saint Germain topped the group, ending their campaign with a 1-1 draw away at Ukrainian outfit Karpaty Lviv.
Napoli took the phrase last chance saloon to its limits also on Wednesday as a goal from in-form Uruguayan international striker Edinson Cavani in the third minute of time added on gave the Serie A side a 1-0 win over Romanian outfit.
The win lifted Napoli over the unfortunate Romanians and fill second spot behind group winners Liveprool, who drew 0-0 at home to Utrecht.
Dortmund had got the ideal start in Seville as Japanese striker Shinji Kagawa struck in the fourth minute.
However, Ivory Coast international Romaric drew the hosts level just after the half hour mark reacting first after the ball came off the chest of Brazilian team-mate Luis Fabiano.
Sevilla took the lead four minutes later in the 35th minute as Malian striker and club captain Fredi Kanoute headed home - however he had to leave the fray in the 41st minute injured.
The German visitors fought back to level the match in the 49th minute. Serbian international central defender Neven Subotic powered a header home, but chances were few and far between from then on and Dortmund were left to focus solely on maintaining their domestic league lead.
Greek side PAOK had gone into the final match requiring just a draw away over Croatian opponents Dinamo Zagreb, who needed a win to progress.
However, it was PAOK who took the second and last qualifying place in Group D with a hard-earned 1-0 victory, all the more impressive as it came only a day after a group of VIP's travelling with them had their bus attacked by home fans.
A goal on the hour by Greek international Dimitrios Salpingidis split the sides and extended the hosts miserable record in European competition which has seen them fail to play European football after the New Year since 1970.
Thursday's play sees holders Atletico Madrid praying for a miracle to retain their hopes of defending their crown as they need to beat already qualified Bayer Leverkusen in Germany and Greek outfit Aris fail to beat Norwegian opponents Rosenborg in Greece.