UEFA say Panathinaikos face a one-season ban from European competition if they fail to pay creditors this month.
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Vladan Ivic was taken to hospital for treatment after the incident, which followed a 54th-minute brawl involving several players.
The former Brazil midfielder, a key member of the 2002 World Cup-winning side, was in the role for only seven months.
Celta Vigo claimed their place in the last 32 of the Europa League with a straightforward 2-0 win over Panathinaikos in Athens.
Greek giants Panathinaikos have fired coach Andrea Stramaccioni following a series of disappointing results.
Manchester United's troubles away from home in Europe continued in a 2-1 defeat at Fenerbahce in the Europa League as Paul Pogba limped off injured.
Manchester United laboured to a 1-0 Europa League victory over Zorya Luhansk at Old Trafford as Zlatan Ibrahimovic headed home in the second half.
Jairo Riedewald scored the winner as Ajax came from behind to record a 2-1 Europa League victory at Panathinaikos.
Dijon have signed Algeria international Mehdi Abeid on a three-year contract.
West Ham suffered more jitters in Giurgiu as they were held to a 1-1 draw in the first leg of their Europa League playoff on Thursday.
Greece's sports minister has postponed the start of top-tier league matches for more than two weeks because of fears of violence.
PAOK held Panathinaikos to a 1-1 draw on Tuesday to win the Greek league playoffs and earn a place in the qualifying round of the Champions League.
Panathinaikos has been docked three points and fined for the fan violence that forced the referee to abort a Greek league match against Olympiakos.
The Greek league match between Panathinaikos and archrivals Olympiakos was postponed on Saturday after home fans clashed with police.
Panathinaikos have appointed Andrea Stramaccioni as their new coach, the Greek giants announced on Monday.
Olympiakos will enter the Champions League groups draw on Thursday despite match-fixing allegations.
The draw for the third qualifying round of the Champions League and some of the bigger clubs join the competition.
Udinese have rewarded goalkeeper Orestis Karnezis with a one-year contract extension after a strong first season in Serie A.
Former Chelsea midfielder Michael Essien has signed for Panathinaikos after leaving AC Milan.
Manchester United could face a tricky Champions League playoff against the likes of CSKA Moscow, Lazio, Monaco or Sporting Lisbon in August.
Riots, violence and local pride on the line: Michael Yokhin goes inside Panathinaikos vs. Olympiakos, the "derby of the eternal enemies."
Panathinaikos have lost their appeal against a three-point deduction for fan violence at a Greek league match against Olympiakos.