PSV Eindhoven lost 1-0 at home to Chornomorets Odesa on Thursday in the Europa League to become the biggest name to crash out of the competition.
Dynamo Kiev avoided the same fate with a 3-1 win over Rapid Vienna, ensuring the Ukrainian giant joined Swansea, Slovan Liberec, Chornomorets, NK Maribor and Maccabi Tel Aviv in reaching the knockout stage on the final night of group play.
Tottenham, which beat Anzhi Makhachkala 4-1 behind Roberto Soldado's three goals, and Red Bull Salzburg were the only teams to finish the group stage with perfect records.
The draw for the last 32 is Monday and will contain the eight teams that placed third in their Champions League groups - Juventus, Ajax, Benfica, Napoli, Porto, Shakhtar Donetsk, Viktoria Plzen and Basel.
PSV is a former European champion and winner of the UEFA Cup - the pre-cursor to the Europa League - but has fallen on hard times and is languishing in 10th place in the Netherlands' Eredivisie after Saturday's 6-2 loss to Vitesse Arnhem.
Phillip Cocu's side also has exited the Dutch Cup and is out of Europe thanks to Franck Dja Djedje's 59th-minute goal for Chornomorets, which qualified from Group B with Ludogorets Razgrad. PSV is without a victory in more than two months.
Like PSV, Dynamo Kiev has been more accustomed to playing in the Champions League over the past two decades but is no longer the force of old.
Kiev just had enough to creep into the knockout stage as runner-up from Group G, though, recovering from conceding early against Rapid to ease to victory thanks to goals by Jeremain Lens, Oleg Gusev and Miguel Veloso.
Swansea lost 1-0 at St. Gallen, with Marco Mathys scoring the winner, but advanced as the runner-up in Group A because Kuban Krasnodar only drew 1-1 at Valencia, which had already sealed top spot.
The Swans became the second team from the English Premier League to progress, with Tottenham having already qualified before its thrashing of Anzhi. Lewis Holtby's stylish finish added to Soldado's hat trick as Spurs secured a sixth straight win in Group K.
Wigan failed to join them after losing 2-1 at Maribor, which climbed from last place to runner-up in Group D above Zulte Wagerem on goal difference. Zulte lost 2-0 at home to Rubin Kazan.
Maccabi Tel Aviv sealed runner-up spot in Group F with a 1-0 home win over Bordeaux and Slovan Liberec beat Freiburg to second place in Group H - behind Sevilla - with a 2-1 win at Estoril-Praia.
Fiorentina went through as the unbeaten Group F winner after a 2-1 win against FC Dnipro.