Paris St Germain joined Arsenal in progressing from Group A, while Atletico Madrid and Bayern Munich also took three points to seal the top two spots in Group D.
PSG defeated a plucky Basle 2-1 when Thomas Meunier hit a technically beautiful 20-yard volley in the closing seconds.
His shot had earlier been steered home by Blaise Matuidi before Luca Zuffi produced a brilliant long-range response that dipped under the crossbar after clearing the goalkeeper.
The Swiss side had gone down to 10 men at that stage, with two late cautions for Sergey Die.
Atletico left it late at the Vicente Calderon, Antoine Griezmann firing home his second goal in the third minute of stoppage time to see off battling Rostov 2-1.
The Frenchman had opened the scoring inside half an hour but Sardar Azmoun’s equaliser looked to have salvaged a point for the Russians.
Bayern came from behind to win by the same scoreline at PSV Eindhoven.
The Eredivisie side came out confidently and took the lead through Santiago Arias but they could not contain Robert Lewandowski.
The Poland international scored a penalty, added a second from open play and also rattled the frame of the goal on three separate occasions.
Benfica moved top of Group of B, Eduardo Salvio earning a 1-0 win over Dynamo Kiev from the penalty spot.
Junior Moraes had the chance to level from the spot but Ederson made the save.
Besiktas held visiting Napoli, Ricardo Quaresma's 79th minute penalty giving the Turkish side a lead for just three minutes before Marek Hamsik struck.
