Russian club Zenit St. Petersburg are facing a UEFA racism charge after their fans displayed a large banner with convicted war criminal Ratko Mladic.
The demolition made Atlanta the first Italian side to score and win at Goodison and was only their second away win in Europe.
After a blowout home loss to Atalanta, Everton desperately needs to find a permanent leader and move on from caretaker manager David Unsworth.
AC Milan booked their place in the Europa League's final 32 with a 5-1 win over Austria Vienna on Thursday night.
A "hurting" Everton caretaker manager David Unsworth criticised an unacceptable performance in the 5-1 Europa League home defeat to Atalanta.
Everton's season, like their search for a manager, continues to drift.
Mario Balotelli scored twice as Nice qualified for the Europa League round of 32 by beating Zulte Waregem 3-1 on Thursday.
Gunners still clinched top spot in Group H thanks to a 0-0 draw between BATE Borisov and Red Star Belgrade.
Arsene Wenger's curious decision to play Calum Chambers(5/10) at wing-back backfired as Arsenal were upset by Cologne in Europa League action.
Gunners finished first as Red Star Belgrade and BATE Borisov could only draw 0-0 in group's other game.
David Unsworth has emphasised he does not need a timeframe to be put on his stint as Everton's caretaker manager.
Everton have been fined £26,600 by UEFA after a fan attempted to punch Lyon's Anthony Lopes while holding a child during last month's clash.