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.
Liverpool went through as winners of a tight Group A after beating Udinese 1-0 in Italy, while Anzhi Makhachkala also scraped into the knockout stages despite falling to a 3-1 defeat at Young Boys.
Jordan Henderson scored the only goal for Liverpool in the 23rd minute, but Udinese substitute Antonio Di Natale missed a late chance which could have eliminated Brendan Rodgers' men.
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. One more goal - or a Udinese equaliser - would have seen the Swiss side qualify.
Steaua Bucharest went through as winners of Group E despite being held to a 1-1 draw by FC 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.
Two goals from Cheick Diabate saw Bordeaux confirm their status as Group D winners with a 2-0 win over fellow qualifiers Newcastle.
Also 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.
Two goals from Sergio Floccari helped Lazio secure top spot in Group J with a 4-1 win in Maribor. Libor Kozak and Stefan Radu also scored for the visitors before Marcos Tavares hit a late consolation.
Tottenham joined the Italians in the last 32 but only after two late goals settled their nerves and saw off visitors Panathinaikos, who needed a win to ensure they pipped the Londoners to second place.
Emanuel Adebayor put Spurs ahead on 29 minutes but a 54th-minute equaliser from Zeca caused anxious moments before keeper Orestis Karnezis put through his own goal on 76 minutes and Jermain Defoe wrapped up a 3-1 win.
Basle grabbed the goalless draw they needed in Genk to progress along with the Belgians from Group G. Videoton's match at Sporting Lisbon was postponed until Friday due to a waterlogged pitch, but Basle's point rendered the outcome irrelevant.
With both sides having already qualified from Group L, Levante and Hannover played out a 2-2 draw in Spain, with the Germans blowing a 2-0 lead but still taking the point they needed to top the group.
Lars Stindl and Didier Ya Konan put the visitors in front before the half-hour mark but the hosts hit back after the break with Angel pulling one back on 49 minutes and Vicente Iborra hitting an injury-time leveller.
Also in Group L, Helsingborg won 3-1 at FC Twente in a match between two sides who were already eliminated. Nikola Djurdjic, Alejandro Bedoya and Thomas Sorum scored for the visitors before Dusan Tadic replied for the hosts.
Group H winners Rubin Kazan settled for a 1-1 draw at Partizan Belgrade. Aleksandar Markovic put the hosts ahead on 53 minutes and Salomon Rondon equalised for the Russians five minutes later.
Also in Group H, Inter Milan, already assigned the runners-up position, drew 2-2 at home to Neftci. Marko Livaja's two goals for Inter were cancelled out first by Rashad Sadygov, then by Nicolas Canales one minute from time.
With Group K already settled, Deni Alar's 13th-minute goal gave Rapid Vienna their first points with a 1-0 win over Metalist Kharkiv. Runners-up Bayer Leverkusen beat Rosenborg 1-0 with a goal from Julian Riedel.
Goals from Mouhamadou Sarr and Yassine Benzia gave Group I winners Lyon a 2-0 win over Hapoel Kiryat Shmona, while second-placed Sparta Prague played out a goalless draw at Athletic Bilbao.