Liverpool went through as winners of a tight Group A after beating Udinese 1-0 in Italy, meaning they join Anzhi Makhachkala in the knockout stages.
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 a 3-1 victory over Anzhi Makhachkala , 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.
Late strikes eased a tense atmosphere at White Hart Lane as Tottenham survived a second-half fightback to win 3-1 against Panathinaikos and progress to the knockout stages of the Europa League.
Needing just a draw to progress, Spurs had an air of complacency about them in the opening period, which Panathinaikos controlled for large parts. Emmanuel Adebayor put Tottenham ahead just before the half hour, but the Greeks, who have never won in Britain, played the better football and deservedly equalised through Zeca just after the re-start.
Panathinaikos, knowing victory was their only means of qualifying for the knockout stages, threw everything at Tottenham and looked the more likely to score before Clint Dempsey - whose shot went in after hitting both the bar and keeper Orestis Karnezis - and Jermain Defoe settled the game late on.
First Dempsey's header home Kyle Walker's cross made it 2-1 and Defoe killed the game off with his 13th goal of the season with seven minutes left.
Sergio Floccari scored twice as Lazio confirmed themselves as winners of Group J with an emphatic 4-1 win over Maribor in Slovenia.
Vaclav Prochazka scored the only goal of the game in the 26th minute as Viktoria Plzen beat holders Atletico Madrid 1-0 to qualify for the knockout stages of the Europa League as Group B winners.
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.
Teenage striker Marko Livaja struck twice but a youthful Inter Milan signed off from Group H with a 2-2 home draw against Neftchi at the San Siro. Nicolas Canales stole a share of the points for the Azerbaijan side two minutes from the end to punish Inter's profligacy.
Two goals in five minutes offered some temporary light amid the gloom of a dull 1-1 draw between Partizan Belgrade and Rubin Kazan which changed nothing for either team in Group H.
Kazan had already qualified for the last 32 as group winners while their Serbian hosts could not make it through. It was essentially a dead rubber and that showed in a poor game which rose from its stupor for five minutes after half-time when Sasa Markovic put the hosts ahead before Jose Salomon Rondon levelled.
Genk and Basel played out a dire goalless draw as the pair progressed. The two sides knew a draw would suit them both and there were precious few moments of excitement in a painfully tedious Group G clash.
The Belgians, already through, topped the pool and Basek got the point they needed to seal second spot ahead of Hungarian side Videoton, whose meeting with Sporting Lisbon was postponed because of a waterlogged pitch.
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.
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.
Hannover secured first place in Group L as they held on to claim a 2-2 away draw at Levante.The hosts needed a victory to overhaul the Bundesliga side at the top of the group, but had a mountain to climb after just 26 minutes as goals from Lars Stindl and Didier Ya Konan put Hannover in a commanding position.
Hannover could have been even further in front by half-time had it not been for some sensational goalkeeping by Keylor Navas, but Levante were given a lifeline four minutes after the break when Angel volleyed home from Vicente Iborra's knockdown.
However, Juan Ignacio Martinez's men couldn't find the second goal they really needed to make the Germans sweat until deep into stoppage time when Iborra rose highest to head Jose Barkero's corner into the bottom corner.
Helsingborg gave coach Aage Hareide the perfect send-off with a 3-1 victory over FC Twente in their final Group L fixture at Arke Stadion.
Neither team could progress to the knockout stage but the Swedish visitors were desperate to end on a positive note for Hareide, who will be replaced by Roar Hansen in the new year. And they did just that thanks to goals from Nikola Djurdjic, Alejandro Bedoya and Thomas Sorum, with Dusan Tadic scoring a consolation for Twente.
Lyon continued their dominance of Group I as they beat Hapoel Kiryat Shmona 2-0 at the Stade Gerland.
Already guaranteed top spot after winning four of their previous five matches, Lyon were made to work for their win with home stopper Anthony Lopes needing to be in top form. Mouhamadou-Naby Sarr put Lyon in front early on before Yassine Benzia doubled their advantage in the second period.
The last ever European game at San Mames turned out to be an anti-climax as Athletic Bilbao and Sparta Prague could not muster a goal between them in a 0-0 draw that saw Sparta progress at the expense of the Basque side.
Julian Riedel scored a debut goal to earn an under-strength Bayer Leverkusen a 1-0 victory at home to Rosenborg in the Europa League. The 21-year-old finished from close range midway through the second half to settle the Group K dead rubber.
Leverkusen were already guaranteed second place, while their Norwegian opponents' hopes of progression were over, and both teams played like there was little at stake in the first half.
Ten-man Rapid Vienna belatedly broke their Europa League duck as Deni Alar's first-half strike secured a 1-0 upset win over Group K winners Metalist Kharkiv.
The Austrian side had failed to pick up a single point before Thursday's final group game and they were forced to secure a maiden win the hard way after playing the second half a man short.