Police used teargas in an attempt to restrain fans who rushed on to the field after Galatasaray midfielder Felipe Melo was shown a red card, CNN Turk said.
Galatasaray were leading 2-1 in the third minute of added time when the match was halted, sending the players sprinting for the safety of the locker rooms.
The match was the first Istanbul derby of the season and follows months of civil unrest in Turkey's largest city over government plans to demolish a city park at the central square of Taksim.
Besiktas' politicised fan base, dubbed 'Carsi', was a prominent force in the anti-government protests and often clashed with police during the peak of the unrest in June.
At Sunday's match, Besiktas fans chanted, "Everywhere is Taksim, everywhere is resistance," a popular chant from the park protest, CNN Turk reported.