More than 140 arrested over Amsterdam metro vandalism before Ajax and AEK Athens clash
Supporters clashed after trains containing fans of the opposing clubs stopped next to each other en route to the stadium.
Fans also clashed with police in the city centre.
Following the incidents, a station was evacuated to ensure trains containing AEK fans could pass safely, Dutch public broadcaster NOS reported.
The Mayor of Amsterdam Femke Halsema was quoted by NOS as saying the incidents were "a blemish on an exciting football evening that Ajax fans enjoyed a lot."
Crowd trouble has affected Dutch football several times this year, with league games being abandoned in April and May after projectiles, including smoke bombs, were thrown onto the pitch by spectators.
Ajax secured third place in Group B with victory on Thursday and will drop down to the Conference League knockout round playoffs. AEK, who finished bottom of the group, are out of European competition.