Doubles from Bryan Cristante and substitute Andreas Cornelius launched Atalanta into the knockout stages with a 5-1 win as Everton turned in another appalling Europa League performance.
Former AC Milan youngster Bryan Cristante slotted in an early opener and made the points safe when he headed home after the hour
Captain Alejandro Gomez also missed a penalty for Gian Piero Gasperini's side, which is level on 11 points with Lyon. Group E's dominant teams will play to settle top spot in Bergamo on December 7.
READ: Arsenal tops group despite going down to Cologne
Everton's involvement in the competition seemingly cannot end soon enough, with Sandro Ramirez's fine first goal for the club in the 71st minute coming as scant consolation for a sparse Goodison Park crowd.
Along with beleaguered caretaker boss David Unsworth it endured a late salvo from its Serie A opponents that began in the 86th minute when Robin Gosens brilliantly clattered in from long-range via the post.
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One-time Cardiff City misfit Cornelius then twice capitalised on defending pitched some way south of shambolic, leaving Unsworth's long-term job prospects in tatters.
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