AEK Athens has also been ordered to play its next two UEFA competition home games behind closed doors and fined €80,000.
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UEFA said its disciplinary body ordered AEK to pay Bayern €10 euros for each of the 3,288 tickets sold to away fans for an October UCL match.
Both teams were out of contention for the knockout stage, and Benfica had already secured third place and a spot in the Europa League.
Riot police clashed with Ajax fans in the Olympic Stadium before the Group E match, leaving some supporters with blood pouring down their faces.
Ajax Amsterdam reached the Champions League knockout stages for the first time since 2006 after a 2-0 win over AEK Athens.
No arrests or injuries were immediately reported, but images showed supporters left bloodied and an explosion going off before kickoff.
Robert Lewandowski scored once in each half to give Bayern Munich a 2-0 victory over AEK Athens in the Champions League on Wednesday.
Javi Martinez scored after 61 minutes and Robert Lewandowski tapped in two minutes later for Bayern's second win in three group matches.
Benfica played the entire second half with 10 men and squandered a two-goal lead before claiming a thrilling 3-2 win away to AEK Athens.
Nicolas Tagliafico scored two second-half goals as Ajax marked their return to the Champions League group stages with a 3-0 victory over AEK Athens.
Juventus will face Man United in the Champions League group stage this season, giving Cristiano Ronaldo a chance to play against his former team.
Ajax qualified for the Champions League group stage on Tuesday for the first time in four years. AEK Athens and Young Boys also booked their spots.
Arsenal defender Sokratis Papastathopoulos and AEK Athens players have pledged to donate blood and give money in support of those affected.
Greek Superleague disciplinary committee has also docked the club three points and fined them €63,000.
PAOK president Ivan Savvidis has apologised for storming the pitch during Sunday's clash with AEK Athens while appearing to carry a gun.
Greece's sports minister says Greek Super League matches have been suspended indefinitely after the gun-toting owner of PAOK marched onto the pitch.
A disputed goal in a Greek league match on Sunday between AEK and PAOK led to a pitch invasion by one of the team owners, who appeared to have a gun.
Newcastle Jets have lured Argentinian winger Patricio Rodriguez to the A-League, joining former AEK Athens teammate Ronald Vargas at the club.
AC Milan were made to wait for confirmed qualification from the Europa League group stage after being held to a 0-0 draw at AEK Athens.
About 100 AEK Athens and AC Milan fans clashed before the teams' Europa League game in the Greek capital, police say.
PAOK will also play seven home games behind closed doors and pay a fine of €282,500.
PAOK won the Greek Cup by defeating AEK Athens 2-1 in a final marred by violent clashes between fans that injured more than 40 people, two seriously.
Former England international Joleon Lescott has left AEK Athens after less than three months.
Joleon Lescott has left Aston Villa and joined AEK Athens on a two-year deal, the Greek Superleague club have announced.
West Ham avoided a false start at the London Stadium with a 3-0 Europa League qualifying win over Slovenian minnows NK Domzale on Thursday.