Twice UEFA Cup winners Sevilla failed to reach the knockout phase Thursday after a 1-0 defeat at Sampdoria eliminated the Spaniards.
Sampdoria's victory sent them through from Group C along with VfB Stuttgart, who thumped group winners Standard Liege 3-0 in their final game to progress to Friday's last 32 draw.
Paris St Germain, twice winners Tottenham Hotspur, NEC Nijmegen and Olympiakos Piraeus also sealed their place in the first knockout round.
Back-to-back winners of the competition in 2006 and 2007 under coach Juande Ramos, Sevilla are only the second side since the group stage format was introduced in the 2004-05 season to miss out on qualification after accumulating six points.
Substitute Jonathan Bottinelli scrambled in a 74th minute winner for Sampdoria, who extended their unbeaten run at home in Europe to 12 games. Samp and Stuttgart finished with seven points, two points behind Liege.
Stuttgart's qualification, earned with goals from Sami Khedira, Roberto Hilbert and Ciprian Marica, came as a major boost for head coach Markus Babbel whose future was been placed in doubt Tuesday when the German FA said it would only allow him to manage the club until the end of the season.
The former Stuttgart assistant coach took over as team manager last month after the sacking of Armin Veh but does not have the qualifications to coach in Germany's top division.
Paris St Germain grabbed the one remaining place from Group A on goal difference from Racing Santander but their 4-0 demolition of Twente Enschede was overshadowed by fighting between rival fans in Paris before the match.
French police reported that clashes took place in the centre of the French capital with one Twente fan requiring hospital treatment after being injured by a hatchet.
"It was a small street fight which took place around 4pm," a police spokesperson said, adding there were around 200 fans from each side involved.
Peguy Luyindula scored twice for PSG as their margin of victory meant that Racing Santander's 3-1 win at home to Manchester City proved academic.
Spurs hit back from 2-0 down to draw 2-2 at White Hart Lane with Spartak Moscow, who exited the competition after NEC's late 2-0 victory over Group D winners Udinese.
Spurs, unable to play ineligible striker Roman Pavlyuchenko against the side they signed him from in September, fell behind to two first-half goals from Artem Dzyuba but Croatian Luka Modric, with his first goal for the club, and a Tom Huddlestone header hauled the Premier League side level after the break.
Olympiakos's 4-0 rout of Hertha Berlin sent the Greek side through from Group B.