Andrea Petagna's early strike saw Atalanta complete an unbeaten Europa League group-stage campaign with a 1-0 win over Lyon on Thursday, while AC Milan were beaten by Rijeka in Croatia.
Atalanta, coming off the back of a stunning 5-1 win at Everton a fortnight ago, edged out in-form Lyon to finish top of Group E as former Milan striker Petagna scored his fourth goal of the season in the 10th minute.
The visitors failed to find an equaliser despite fielding a strong side powered by Memphis Depay, Nabil Fekir and Mariano Diaz, and could now be drawn to face one of the eight sides slipping down from the Champions League in the last 32, including Atletico Madrid and Napoli.
Everton made it two wins out of two under new manager Sam Allardyce by cruising to a 3-0 victory over Apollon Limassol in Cyprus, although the former England boss did not travel with the squad due to a medical appointment.
Forward Ademola Lookman, 20, scored a double with close-season signing Nikola Vlasic adding a late third to salvage some pride for Everton as they avoided finishing bottom of the group.
"It's been good (under Sam Allardyce). Different training, different tactics. I'm enjoying it," Lookman told BT Sport.
"Previously with the results and mood in the camp, players' confidence wasn't as high as it is now. We're getting there."
Gennaro Gattuso is still waiting for a first win as Milan head coach after a 2-0 loss at Rijeka.
Milan had already wrapped up top spot in Group D, while Rijeka missed out on joining the Italian giants in the last 32 as AEK Athens pipped them to second courtesy of a 0-0 draw at Austria Vienna.
There was heartbreak for Moldovan side Sheriff Tiraspol, as they slipped from first to third in Group F after a 2-0 loss at FC Copenhagen, dropping below the Danes and Lokomotiv Moscow.
Bulgarians Ludogorets took the second spot in Group C behind already-qualified Braga with a 1-1 draw at Hoffenheim.