Marseille will meet Atletico Madrid in the final in Lyon on May 16 after the Spanish side beat Arsenal 1-0 with a goal from Diego Costa to win 2-1 on aggregate.
The result also meant Arsenal will not qualify for the Champions League for a second straight season.
The winner between Madrid and Arsenal will likely play Marseille, who beat Salzburg 2-0 in their first leg with goals from Florian Thauvin and Clinton N'Jie.
Atletico, the 2010 and 2012 winner, will travel to London for the first leg against Arsenal who have never won the Europa League or the UEFA Cup.
Marseille progressed after a 2-1 win at Athletic Bilbao that was marred by crowd trouble. Lazio advanced with a 2-0 win at Dinamo Kiev and Leipzig drew 1-1 at Zenit.
There was another surprise in Germany where two goals from Valon Berisha led Salzburg to a 2-1 victory at Borussia Dortmund.
Athletic Bilbao are scheduled to next face Marseille, while Borussia Dortmund will take on Austrian side Salzburg.
Shockingly, Serie A leaders Napoli weren't good enough to advance in the Europa League on Thursday after they were knocked out in Germany by RP Leipzig.
Arsenal powered past Ostersund 3-0, Atletico Madrid thrashed Copenhagen 4-1 and Italian league leader Napoli slipped to a surprise 3-1 home defeat against Leipzig.
Gurpreet, however, said he would go back to European clubs if it meets his terms and conditions.
In other ties, Scottish club Celtic F.C will host Russian club Zenit St Petersburg, Napoli will play RB Leipzig, Ludogorets will take on seven-time European champions AC Milan.
Lyon routed Apollon 4-0 and Atalanta hammered Everton 5-1 in Goodison Park, leaving the Premier League side winless, to confirm their dominance in Group E.
With several young players, including Reiss Nelson, Joseph Willock and Ainsley Maitland-Niles, the Gunners didn't look dangerous until Giroud's goal.
Within 25 minutes, Arsenal was a decisive 3-0 up through two goals by Theo Walcott and Rob Holding.
Milan returns to UEFA competitions after a three-year absence and avoided long travel for Thursday games that lurk in the 48-team draw.
Phil Jones and Daley Blind were fined 5,000 euros ($5,900), while Jones was also suspended for two European games after abusing a UEFA doping control officer.
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