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 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, who are level on 11 points with Lyon. Group E's dominant teams will play to settle top spot in Bergamo on December 7.
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 they endured a late salvo from their Serie A opponents that began in the 86th minute when Robin Gosens brilliantly clattered in from long-range via the post.
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.
GOOOOOOLLLLLLLLL!!! ANDREAAAASSSS CORNELIUUUUSSSS— Atalanta B.C. (@Atalanta_BC) November 23, 2017
A much-changed Everton side captained by Wayne Rooney started on the front foot before being cut apart with galling ease in the 12th minute.
Timothy Castagne got to the byline and, when Ashley Williams failed to clear his low cross, Cristante was left with a simple finish.
Kevin Mirallas benefited from some similarly generous Atalanta defending as the half hour approached but the angle was against him as he shot too close to goalkeeper Etrit Berisha.
The same could not be said for Sandro, who hacked wildly over on the follow-up.
Andrea Masiello made a magnificent headed block on the goalline in the 38th minute to deny Everton youngster Tom Davies an equaliser but the centre-back was limping heavily by first-half stoppage time – his condition compromising a clearance than almost allowed Mirallas to level matters.
Williams sparked an on-field melee in Everton's last Europa League home game against Lyon and another inauspicious outing for the Wales defender took a further wrong turn early in the second period.
Cristante stole clear of Williams, who responded with a desperate lunge that left referee Jakob Kehlet with little option other than to point to the spot.
But Joel Robles came to Everton's aid, springing to his right to keep out a poor penalty from Gomez, who failed to convert the rebound.
Williams kept his goalkeeper busy by glancing a left-wing corner towards his own goal moments later. Joel saved brilliantly once more and Jonjoe Kenny denied Cristante on the line.
Everton's other centre-back Michael Keane was not having a much more enjoyable evening and crumpled to the floor when confronted shoulder-to-shoulder by Hans Hateboer, although the Atalanta wing-back's resulting shot was deflected behind.
The visitors' earlier corner routine paid dividends in the 64th minute when Gomez again threatened the near post from the left and Cristante glanced his seventh of the season into the net.
Atalanta's boisterous travelling support proceeded to shake the Bullens Road stand with prolonged celebrations.
Their din was only briefly punctuated by Sandro arrowing a brilliant finish across Berisha into the bottom corner.
That Everton briefly threatened to complete a comeback felt like a trick of the mind as Cornelius made merry in the closing minutes, cutting in to finish sharply before punishing more dismal set-piece defending after fellow sub Gosens had spectacularly sapped any remaining resistance.
|LaLiga match set for USA following groundbreaking Relevent deal|
|FIFA rankings: France number one, Croatia and England soar, Germany and Argentina plummet|
|Hansen hails ´big leader´ Whitelock ahead of 100th cap|
|Cipriani pleads guilty to common assault and resisting arrest|
|PSG snap up Kehrer from Schalke|
|Maitland-Niles facing two months out with broken leg|
|Walker backs City squad strength to overcome De Bruyne blow|
|Thomas & Froome skip Vuelta, named in Tour of Britain squad|
|Thurston rules out retirement U-turn|
|Pumas look to build on Jaguares progress in Rugby Championship|
|Super Cup glory will make Atletico strong - Simeone|
|Rugby Championship 2018: True status of Erasmus´ Springboks rebuild to be discovered|
|LaLiga 2018-19: Coutinho ready to be Barca´s next Brazilian superstar|
|Serie A 2018-19: Can Napoli, Roma, Inter or AC Milan overhaul Juventus?|
|Braves survive skirmish, loss of Acuna to top Marlins|
|Robertson handed surprise start, Hodge gets nod for Bledisloe opener|
|MLS Review: Wayne´s World as Rooney inspires DC United, LAFC win|
|Djokovic and Dimitrov survive but Zverev loses in Cincinnati|
|Rain halts Halep as Muguruza´s defence ends and Wozniacki retires|
|Ozil´s racism claims nonsense, says Kroos|
|Malcom lost for words after Camp Nou bow alongside Messi|
|Injured Fowler withdraws from play-off opening Northern Trust|
|Marcelo happy with Madrid squad amid transfer talk|
|Foles isn´t worried about Brady´s handshake snub|
|Eli Manning on Jalen Ramsey´s comments: ´Who?´|
|Cerezo: Atletico´s objective is to reach Champions League final|
|Judge´s recovery taking longer than expected|
|Ronaldo in the past as Casemiro backs Lopetegui after Madrid loss|
|With our ´cojones´ Atletico can beat anyone – Costa revels in Super Cup glory|
|Super Cup loss doesn´t change Real Madrid transfer policy, says Lopetegui|
|Griezmann: Super Cup triumph justifies staying at Atletico|
|Valverde defends Suarez performances|
|Simeone´s eclipses Aragones as Atletico´s top coach with seventh title|
|Rockets GM: LeBron James is ´the greatest ever´|
|Salihamidzic, Kovac not standing in way of Rudy exit|
|Jaguars DB Ramsey calls Bills QB Allen ´trash´|
|Real Madrid 2 Atletico Madrid 4 (after extra time): Saul stunner seals Super Cup glory|
|Ex-India Test captain Wadekar dies aged 77|
|Gundogan ready to step up in absence of injured De Bruyne|
|Djokovic overcomes illness to see off Mannarino|
|Diego Costa nets fastest UEFA Super Cup goal ever|
|Everton feared missing out on Mina after World Cup strike|
|Barcelona 3 Boca Juniors 0: Messi, Malcom net as Barca win Joan Gamper Trophy|
|All Blacks stick with Barrett as Mo´unga misses out altogether|
|Modric benched for UEFA Super Cup clash with Atletico Madrid|
|Cipriani charged with assault after Jersey nightclub incident|
|Hamburg 1 Bayern Munich 4: Wagner and Muller hit braces in comeback victory|
|WATCH: Messi scores first goal as Barcelona captain|
|Iniesta, Xavi and Puyol were great teachers, says new Barcelona captain Messi|
|Moses retires from international football|
|Goals, assists, set-pieces - The stats that show De Bruyne is almost irreplaceable for City|
|Bergeron wins mammoth 24-man U.S. Amateur play-off|
|Hart to Burnley "not rocket science", says Dyche|
|Leipzig, Schalke reject Rudy transfer rumours|
|Yedlin knee injury not serious, Newcastle confirm|
|Bartomeu satisfied with Barcelona squad amid Pogba links|
|Kevin De Bruyne suffers knee injury|
|Steelers QB Roethlisberger in concussion protocol|
|Kehrer to PSG not complete, say Schalke|
|Hopoate handed 10-year ban from NSWRL|
|Is this worth it? Injuries prompted Te´o to consider future|
|Croatia hero Subasic retires from international football|
|Iniesta makes it two in two for Vissel Kobe|
|Chelsea send out defensive duo on loan|
|Zaha 2023: Palace star means more than goals|
|De Jong set for Ajax stay despite Barcelona interest|
|Serena ´still at the very beginning´ of comeback|
|Ajax can benefit from Mourinho approach - Blind|
|Foley not convinced by reports All Blacks will drop Barrett|
|Zaha signs Crystal Palace extension|