Lucas Perez grabbed his first hat-trick in an Arsenal shirt as Arsene Wenger's side thumped Basel.
Jose Callejon and Dries Mertens scored second-half goals to earn Napoli a 2-1 victory over Benfica in Lisbon to send the Italians through to the knockout phase as winners of Group B.
Twice former European champions Benfica pulled a goal back late on through Raul Jimenez and qualified as runners-up.
"We reached our objective, we wanted to win the group and we did it with a splendid performance here in Lisbon," said Callejon.
In the group's other game, Besiktas travelled to Ukraine hopeful of advancing after their rousing three-goal fightback on matchday five against Benfica, but the Turkish champions unravelled in a disastrous first half.
Artem Besedin bundled in Dynamo's opener on nine minutes at the Olympic Stadium and Besiktas suffered a critical blow on the half hour with Andreas Beck sent off for a professional foul on Derlis Gonzalez.
Andriy Yarmolenko converted the resulting penalty and the hosts struck twice more before the break through Vitaliy Buyalskiy and Paraguayan Gonzalez to floor the visitors.
Frustrations boiled over as Cameroon striker Vincent Aboubakar was dismissed for a second yellow card on 56 minutes and a miserable evening grew even more humiliating with Serhiy Sydorchuk and Junior Moraes adding their names to the scoresheet.
"We are very, very upset and you can see it from every player?s face in the dressing room. We want to forget this game and want to represent Turkey in the best possible way in the Europa League now," said Besiktas captain Oguzhan Ozyakup.
Lucas Perez grabbed his first hat-trick in an Arsenal shirt as Arsene Wenger's side thumped Basel 4-1 in Switzerland to pip French champions PSG to top spot in their group.
Hobbled by an ankle injury, Perez has played sparingly since his arrival from Deportivo la Coruna in August, but the Spaniard was gifted two simple finishes as the Gunners dominated at St. Jakob-Park.
The Spaniard slotted home his third on 47 minutes and Mesut Ozil set up Alex Iwobi to score a fourth before Seydou Doumbia notched a consolation for Basel.
Ludogorets claimed a memorable point and a place in the Europa League with a 2-2 draw at the Parc des Princes where they twice led on a frustrating evening for Unai Emery's hosts.
Virgil Misidjan headed the Bulgarian outfit into an early advantage, but Edinson Cavani's superb acrobatic effort brought PSG level on the hour.
A mistake from Brazilian centre-back Marquinhos allowed Jonathan Cafu to tee up Wanderson to put Ludogorets back on top, with Angel Di Maria's stoppage-time strike not enough to prevent Arsenal climbing above Paris.
"It's a disappointment. We played a good match at Arsenal (in November) and came back in first place. I think the team deserved to win, but that's football," said PSG coach Emery.
Turkey midfielder Arda Turan hit a quickfire second-half hat-trick to propel Barcelona to a 4-0 win at home to Borussia Moenchengladbach in Group C with Lionel Messi also on target for the Catalan giants.
Celtic's Patrick Roberts scored a terrific solo effort against parent club Manchester City in a 1-1 draw at the Etihad Stadium.
Kelechi Iheanacho staked his claim to a longer run in Pep Guardiola's first team -- with Sergio Aguero facing a four-match ban -- as the Nigerian struck a fine equaliser.
Robert Lewandowski's stunning first-half free-kick ended Atletico Madrid's bid for a perfect six group wins from six as Bayern Munich won 1-0 at the Allianz Arena.
Rostov will continue their European adventure in the Europa League after finishing third in Group D following a goalless draw at PSV Eindhoven.