Lyon sealed top spot in the Europa League standings while Roma survived a red-card scare to reach the last 16 on a chaotic final league-phase night.
Ajax keeper Remko Pasveer made five saves and scored on his own attempt to help the hosts win the shootout as Dutch international Brian Brobbey missed two penalties.
British-born Greece defender George Baldock was found on Wednesday in a swimming pool at his home in the southern Athens suburb of Glyfada.
Panathinaikos reached the Greek Cup quarter-finals after a 3-2 penalty shootout victory over Apollon Kalamaria on Wednesday.
They beat beat local rivals Olympiakos 3-1 to complete the first leg of a possible domestic double.
Panathinaikos secured a Champions League qualifying spot by beating PAOK Salonica 2-0 on Sunday to extend their lead in the Super League playoffs to a eight points with two matches left.
Greek soccer, already plagued by match-fixing and crowd violence, suffered more misery on Tuesday when Panathinaikos lost 4-3 at home to Odense and were knocked out of the Champions League qualifiers.
Tear gas fired by police at rioting protesters outside the Olympic Stadium caused a 25-minute interruption during Panathinaikos's 3-1 win over Atromitos in the Greek Super League on Sunday.
Chelsea completed a clean sweep for English teams in the Champions League group stage after beating Cluj 2-1 on Tuesday to join holders Manchester United, Arsenal and Liverpool in the last 16 of the competition.
Panathinaikos won the Greek title for the first time in six years by beating Iraklis 2-0 on Sunday.
Sweden's Helsingborg and Greek side Panathinaikos became the first clubs to reach the knockout phase of the UEFA Cup on Thursday while former European champions Bayern Munich missed their chance to reach the last 32, a 1-1 draw in Portugal against Braga ensuring the Bundesliga leaders still have work to do to qualify from the group stage.
IMAGES from the Europa League matches played on Thursday.
Jose Mourinho's side top Group G with a maximum nine points, three clear of second-placed Slavia.
Rennes denied late Europa League equaliser due to little-known rule
Liverpool overcame an early scare and came from a goal down to claim a 3-1 win at Austria's LASK Linz.
The move follows a pitch invasion at the end of the Athens derby last weekend and a Super League board meeting which ended in a brawl on Tuesday, with Greece's recently-elected Syriza ruling party aiming to stamp out the problem of crowd violence.
French club Olympique Lyon and Atletico Madrid of Spain booked their places in Thursday's draw for the Champions League group stages with convincing playoff wins on Tuesday.
Former European champions Liverpool and Inter Milan sealed their berths in the Champions League last 16 but last season's finalists Chelsea still have work to do after a 1-1 draw at Girondins Bordeaux on Wednesday.
Juventus returned to the Champions League proper for the first time in three seasons after a 1-1 draw at Artmedia Bratislava gave the Italians a 5-1 aggregate win.
News of all that's transpired on and off the football field
Greece's Football Federation (EPO) could be suspended from international football over government interference should a proposed new sports law be voted in, FIFA and UEFA have warned.
Images from football matches played across Europe over the weekend.
Rodrigo Palacio snatched an 88th minute win for Inter Milan over Partizan Belgrade in the Europa League on Thursday while Lazio were on the wrong end of some late drama in a 1-1 draw at Panathinaikos.
Greece captain Giorgos Karagounis has signed for Fulham on a free transfer, the Premier League club announced on Tuesday.
Malaga gave themselves an excellent chance of qualifying for the Champions League for the first time by beating Panathinaikos 2-0 at home in the first leg of their playoff on Wednesday.
The world's best player Lionel Messi lit up the opening night of the Champions League for Barcelona although holders Inter Milan and Manchester United endured less than sparkling starts on Tuesday.
A Sunderland fan is suing his own club after being knocked out by a stray shot while watching a training session.
'This is about him. This is a reflection of his personality -- don't give up -- his fighting spirit, every player giving everything'
Arsene Wenger spoke in a calm, almost matter-of-fact fashion after his Arsenal side had torn Braga to shreds on Wednesday.
Olympiakos have sacked their Brazilian coach Zico following a string of poor results, the Greek club confirmed on Tuesday.
Panathinaikos could be on the receiving end of a Champions League backlash from a wounded Barcelona on Tuesday after the La Liga giants were stunned 2-0 at fortress Nou Camp by unfancied Hercules at the weekend.
The UEFA Champions League kicks off this week with powerhouses such as favourites Barcelona and holders Inter Milan yet to hit their stride, leaving the door open for nasty surprises in games they would ordinarily win.
Sweden elected to train behind closed doors on Saturday as they prepared for their Euro 2016 opener against Ireland following several flare-ups between players and coaches in training on Friday. Angry words were exchanged between striker John Guidetti and midfielder Albin Ekdal, while Guidetti also argued with assistant trainer Peter Wettergren during Friday's session. This led to the Swedes deciding not to open Saturday's training to the media for the usual 15 minutes.
Celtic and Arsenal will meet each other for a place in the Champions League group stage after being drawn together in the final qualifying round at the draw Friday.
Olympiakos kept their one-point lead over Panathinaikos at the top of the Greek Super League on Sunday courtesy of a 3-0 home win over bottom club Panthrakikos.
Bobby Zamora and Bjorn Helge Riise twice combined to set Fulham on their way to a 3-2 win at snowy Basel on Wednesday, sealing the London club's berth in the final 32 of the Europa League. Hertha Berlin, in last place in the Bundesliga, scraped through thanks to a 1-0 win at home to Group D winners Sporting and Panathinaikos of Greece secured second place in Group F when Djibril Cisse scored two in a 3-0 win over Dinamo Bucharest.
Inter Milan coach Jose Mourinho's fixation with playing three up front will come under further scrutiny at home to Werder Bremen.
Inter Milan coach Jose Mourinho's fixation with playing three up front will come under further scrutiny at home to Werder Bremen on Wednesday following Sunday's 1-0 defeat by AC Milan.
Competition favourites AC Milan will face Werder Bremen, one of the Champions League dropouts, in the last 32 of the UEFA Cup following Friday's draw in Nyon, Switzerland.
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