The Eredivisie giants were in the Greek capital on Tuesday for the latest round of fixtures in Group E.
Before a ball had even been kicked, tempers boiled over off the field as the home support set their sights on the visitors.
A Molotov cocktail, plastic bottles and various other objects were aimed in the direction of those to have made the trip from Amsterdam.
No arrests or injuries were reported at the time, with the local police quickly onto the scene.
Those responsible for the missiles were dispersed, but Ajax followers were understandably left angered by the events which had unfolded.
As a result, they ended up clashing with baton-wielding enforcement officers.
Police had also faced trouble from a number of Greek supporters in central Athens earlier in the day, and on Monday evening.
Petrol bombs were also used during those disturbances, with traffic blocked before order was restored.
As chaos erupted inside the stadium on Tuesday, Ajax defender Matthijs de Light was among those to try and act as peacemaker.
He approached the away end as fans tangled with police and called for calm from those involved.
The Netherlands international has emerged as a talismanic presence at Ajax, with the likes of Barcelona and Manchester City currently being linked with big-money moves for his services.
For now, his focus is locked on trying to steer his current employers into the last 16 of the Champions League.