Both sides had already qualified for the next stage but Plzen's win helped them move above the Spaniards into pole position on 13 points. Atletico had Brazilian Diego Costa sent off in injury time.
Also in Group B, Hapoel Tel Aviv claimed their first win with a 2-0 victory over Academica in Israel. Victor Merey and Hanan Maman scored in the second half, although both sides had already been eliminated.
Anzhi Makhachkala scraped into the knockout stages of Group A despite falling to a 3-1 defeat at Young Boys. Goals from Gonzalo Zarate, Moreno Costanzo and Alexander Gonzalez gave Young Boys victory over Anzhi, who replied through Odil Akhmedov and had Lacina Traora sent off.
Steaua Bucharest went through as winners of Group E despite being held to a 1-1 draw in Copenhagen. Steaua, who had Cristian Tanase sent off after 49 minutes, went ahead through Raul Rusescu before Igor Vetokele hit a late equaliser.
Stuttgart joined Steaua in the knockout stages but missed the chance to go through as group winners as they were beaten 1-0 at home by Molde. Davy Angan scored the only goal in first half injury-time.
In Group D, goals from Goncalo Abreu and Heldon were enough to see Maritimo home with a 2-1 win over Club Brugge, who replied through a Lior Refaelov penalty.
Having already confirmed their place at the top of Group C, Fenerbahce were hammered 3-0 at home by runners-up Borussia Monchengladbach, for whom Tolga Cigerci, Mike Hanke and Luuk de Jong got on the scoresheet.
Cypriots AEL Limassol finished their Group C campaign with their first win, 3-0 over Marseille, with goals from Orlando Sa, Edmar and Dossa Junior. Two goals from Roman Zozulya and further strikes from Nikola Kalinic and Sergey Kravchenko saw Group F winners Dnipro finish with an emphatic 4-0 home win over AIK.
Second-placed Napoli fell 3-1 at home to already-eliminated PSV, despite taking an 18th-minute lead through Edison Cavani. A hat-trick from PSV's Tim Matavz helped the Dutch side finish in style.
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