Former winners Shakhtar Donetsk ensured they were the first team to go through to the knockout stages of the Europa League with a 100% record following a 4-2 win over Braga.
The Ukrainian side, Zenit St Petersburg and Schalke were the only three teams able to advance to the last 32 with a perfect record and Shakhtar did just that after easing to victory in Portugal.
The visitors took the lead on 29 minutes when Serhiy Kryvtsov headed in Marlos' corner before Taison doubled their advantage moments later with a composed finish.
Nikola Stojiljkovic gave the hosts some hope just before the break but Donetsk restored the two-goal cushion through Kryvtsov's second with Taison netting his second on 66 minutes to make it 4-1 before Nikola Vukcevic's late consolation for Braga.
Villarreal eventually overcame 10-man Steaua Bucharest to book their place in the next round thanks to a last-gasp winner from Manu Trigueros.
Nicola Sansone gave the hosts a half-time lead after needing two attempts to get past Steaua goalkeeper Florin Nita.
Vlad Achim levelled for the Romanian side before Gabriel Tamas received his marching orders for two bookable offences with 11 minutes left.
The Yellow Submarine used this to their advantage with Trigueros chipping in a wonderful effort from the edge of the box two minutes from time to snatch all three points.
Kalifa Coulibaly scored a 94th minute winner to put Gent through to the next phase following a tense 1-0 victory at Konyaspor.
In a tight affair with limited chances, Gent were crashing out of the competition through their poor head-to-head record with Braga until the Mali forward brought down Stefan Mitrovic's long ball on his chest before swivelling and unleashing a volley into the bottom corner to send the Belgian side through.
Ten-man Fiorentina advanced to the next round with a 2-1 win over Qarabag in Azerbaijan.
After a goalless first half, Matias Vecino sparked the game into life on 60 minutes to give the visitors the lead before Reynaldo equalised for Qarabag with 17 minutes remaining.
Federico Chiesa restored Fiorentina's lead three minutes later before picking up his second yellow card for holding back Ivan Bebek but the Italian side held on for the three points.
Two late goals put Osmanlispor through as Group L winners after a 2-0 win over Zurich.
Dzon Delarge put the hosts in front on 73 minutes after racing onto Adam Maher's pass before firing a shot into the top corner with Erdal Kilicaslan sealing the points a minute from time with a calm finish.
PAOK advanced after goals from Garry Rodrigues and Dimitrios Pelkas in each half saw off Slovan Liberec in a 2-0 success in Greece.