Cristian Rodriguez struck deep into stoppage time to continue Atletico Madrid's remarkable European run of 14 consecutive victories as they eventually saw off a brave challenge from Viktoria Plzen.
The Czech side had successfully stifled last season's winners throughout and could even have gone ahead themselves when Vaclav Prochazka's brilliant free-kick forced Sergio Asenjo into a fabulous save just before the hour mark.
However, Atletico continued to probe until the final whistle and finally got their reward when Rodriguez received the ball on the edge of the area and gave Matus Kozacik no chance with a sweetly-struck volley - his first goal for the club since joining from Porto.
Also in Group B, Omer Damari struck an injury time equaliser for Hapoel Tel Aviv in a 1-1 draw at Portuguese side Academica, who led through a Salim Cisse effort.
Earlier in the night, Philippe Coutinho's 10th minute strike set Inter Milan on their way to their first win in Group H with a 3-1 success against Neftchi in Azerbaijan.
Inter, who had been held at home in their opening group game by Rubin Kazan, built on their lead with further strikes from Joel Obi and Marko Livaja before half-time. Nicolas Canales scored a 53rd minute consolation for the hosts.
However, Rubin Kazan kept pace with the Italians with a 2-0 home win over Partizan Belgrade. Gokdeniz Karadeniz opened the scoring on the stroke of half-time and Alexander Ryazantsev added a second just after the break.
Back to the late kick-offs and Napoli's excellent start to the new season ran aground in Eindhoven where they were beaten 3-0 by PSV in Group F.
Walter Mazzarri's men went into the game unbeaten in seven but were behind after seven minutes from a Jeremain Lens strike, and Dries Mertens and Marcelo added further goals for the Dutch side.
Dnipro, who had beaten PSV in their opening game, claimed their second straight win as they came from behind twice to beat AIK 3-2 in Sweden.
Goals from Helgi Danielsson and Henok Goitom for the hosts were cancelled out by efforts from Nikola Kalinic and Vitaly Mandzyk before Evhen Seleznyov struck to seal the points seven minutes from time.
Ligue 1 leaders Marseille returned to form in emphatic fashion after the weekend's humiliating defeat to Valenciennes as they beat Cypriots AEL 5-1 in Group C.
Edwin Ouon put the visitors in front but goals from Rod Fanni, Michel Mendes, Andre Gignac and two for Loic Remy saw Marseille home.
There were six more goals in the other Group C tie as Fenerbahce won 4-2 at Borussia Monchengladbach.
Luuk De Jong put the hosts in front but Cristian Baroni hit two and further goals were added by Raul Meireles and Dirk Kuyt, with Igor De Camargo grabbing the Germans' second.
In Group D, Club Brugge beat Maritimo 2-0 with goals from Carlos Bacca and Bjorn Vleminckx.
A late own goal from Ragnar Sigurdsson gave Steaua Bucharest a 1-0 win over FC Copenhagen in Group E, while Jo-Inge Berget and Daniel Chima scored in Molde's 2-0 home win over Stuttgart.
Going back to the early action and Hungarians Videoton pulled off an upset in Group G as they strolled to a 3-0 home win over Sporting Lisbon.
Paulo Vinicius, Filipe Oliveira and Nemanja Nikolic all scored before half-time for the home team, who had slumped to a 3-0 defeat of their own at Genk in their opening group game.
The Belgians had looked well on their way to another win in the other Group G game as they led Basel 2-0 in Switzerland through an early Benjamin De Ceulaer strike and a second from Jelle Vossen.
But the hosts hit back to claim a point in a 2-2 draw thanks to a second half double from Marco Streller, the first of which came from the penalty spot.
Lazio nudged to their first win in Group J - Ederson hitting the only goal of the game in the 62nd minute against Maribor at the Stadio Olimpico. The visitors had Jovan Vidovic sent off late on.
In Group I, Gueida Fofana scored twice, including an injury-time winner, as Lyon earned their second straight win with a thrilling 4-3 triumph over Hapoel Kiryat Shmona in Israel.
Shimon Abuhatzira put the home side in front after just seven minutes before Fofana, Fabian Monzon and Anthony Reveillere put the Frenchmen well in control at the break.
Hapoel clawed back level through Lior Levi and Abuhatzira but when they thought they had done enough to take a point, Fofana struck two minutes into added time.
Last year's runners-up Athletic Bilbao slumped to a 3-1 defeat at Sprata Prague. Tomas Zapotocny, Bekim Balaj and Josef Husbauer scored for the home side, with Oscar De Marcos replying late for Bilbao.
In Group K, Edmar and Cleiton Xavier scored to give Metalist Kharkiv a 2-0 home win over Rapid Vienna, while Stefan Kiessling scored in the 76th minute to give Bayer Leverkusen a 1-0 win at Rosenborg.
Hannover shrugged off the ninth minute dismissal of Turkish defender Karim Haggui to beat Spaniards Levante 2-1 in Germany.
Michel had put Levante in front from the spot after Haggui's red card, but Szabolcs Huszti and Didier Ya Konan struck back to win it for the home side in Group L.
In the same group, two Nikola Durdic goals put Helsingborg 2-0 up against FC Twente but the Dutch side hit back to claim a 2-2 draw with goals from Rasmus Bengtsson and Douglas.
In an early kick-off in Group A, veteran striker Samuel Eto'o scored two late goals to give big-spending Russians Anzhi Makhachkala a 2-0 win over Young Boys.