The match had already been suspended twice during the first half, once for flares on pitch, the other time after a cup was lobbed from the stands.
A double from Santiago Gimenez and one from Igor Paixao had given the team from Rotterdam an unprecedented lead at the Johan Cruyff Arena in Amsterdam.
TV images showed three flares burning on the pitch with smoke from other flares pouring from the notorious south stands of the arena, where the hardcore "F-side" fans sit.
According to Dutch media reports, police used horses and fired tear gas to disperse fans from outside the stadium. Images on social media showed fans attacking the entrance to the stadium.
"After the stopped game supporters broke into the main (stadium) entrance. Order has since been restored," the police said.
"It is a jet black day, this makes it even worse," Ajax coach Maurice Steijn told broadcaster NOS.
Feyenoord manager Arne Slot said it was "especially annoying" that his side were not able to finish what had been a superb performance.
"In this way the chance for something very beautiful is taken away from us," he said on the club website.
"We understand the decision that has been taken, but we do not feel a sense of victory... And so we certainly won't get on the bus satisfied."
The Dutch football association (KNVB) told broadcaster NOS it hoped to make a decision regarding the match on Monday, but added it might take longer.
Slot said that no outcome would be ideal.
"The match will be played with or without an audience, or not and it will be a legal victory for us. Whatever the case, in all cases there is distortion of competition," Slot said.
"The question now is what the KNVB will do to keep this to a minimum."
Ajax have had a miserable start to the season. After winning their first match, they have drawn two and lost one in the Eredivisie. They currently sit 13th in the table.
Defending champions Feyenoord, in contrast, remain unbeaten in the top flight this season.
