Ajax fans came under attack in the Greek capital as home supporters threw flares into the stands housing the Dutch supporters.
Shocking photos showed police officers hitting Ajax fans, leaving some of them caked in blood in the away end.
Footage posted on social media also appeared to show a man leaving the AEK stands to throw a molotov cocktail at the Ajax supporters.
It was reported that Ajax defender Matthijs de Ligt ran over to the visiting fans in an attempt to play the role of peacemaker.
At the start of the second half there were further crowd disturbance as several firecrackers were set off.
Players from both sides were seen to be rubbing their eyes as smoke drifted across the Athens Olympic Stadium.
The trouble comes just three days after the second leg of the Copa Libertadores final between Argentinian rivals Boca Juniors and River Plate was postponed because of fan violence.