Around 100 fans gathered at the hotel where the team was preparing to leave for the Olympic Stadium and demanded that the players travel by taxi instead of the team coach.
The move was a response to the AEK players' decision to leave the stadium by taxi for fear of being attacked following the humiliating 6-0 drubbing by champions Olympiakos two weeks ago.
The AEK players agreed to the demand, taking seven taxis to the Olympic Stadium before beating Atromitos 1-0 thanks to a Roger Guerreiro strike which tightened their grip on third place in the table.
Around 1,500 AEK fans also staged a peaceful protest in the Athens suburb of Nea Filadelphia against the owners of the club.
"Everybody is free to have their opinion," AEK's Spanish coach Manuel Jimenez told a news conference. "I will continue to work as I do every day. A lot has been said but I'm here. The easy thing would be to leave.
"When someone in the family is dying, you do not just let them die if they can be helped. Everyone who is here is trying to keep things going. This club has a long history and we will not leave it to die."
Panionios ensured they would be playing Super League football next season after a 2-1 win at Kerkyra secured their top-flight status with two matches to spare.
Relegated Panserraikos sprang a surprise by defeating second-placed Panathinaikos 1-0 thanks to a Giorgos Georgiadis strike.
Olympiakos, who wrapped up their 38th Super League crown last month, ran out comfortable 3-1 winners over Kavala.
