Footage broadcast on CNN-Turk news channel showed protestors -- some of whom had covered their faces with Palestinian-style checkered kaffiyehs -- hurling incendiary devices at shops and in the streets in the Alibeykoy district in the city's European side.
Protestors threw an incendiary device at a bank in the Sisli district, a bus was set on fire in the Gazi neighbourhood while demonstrators pelted a police station with stones in the downtown Beyoglu, CNN-Turk said.
Riot police fired shots into the air to disperse some 150 protestors who had blocked a highway in Kadikoy district in the city's Asian side across the Bosphorus Strait, the Anatolia news agency said.
Eighty-eight people were detained in 12 separate incidents in Istanbul, the agency added.
The unrest broke out when the activists were prevented from going to the nearby town of Gemlik for a protest rally against the prison conditions of Ocalan, organised by a non-governmental organisation of prisoners' relatives, Anatolia added.
Local authorities had banned the demonstration on the grounds that it was masterminded by Ocalan's outlawed Kurdistan Workers Party (PKK), which has waged a bloody armed campaign against Ankara since 1984.
Police and paramilitary gendarmerie troops, reinforced by forces from neighbouring towns, set up checkpoints at all entrances to Gemlik and stopped some 60 buses bringing in activists from around the country several kilometres (miles) away from the town.
Hundreds of demonstrators boarded the buses to return home after waiting for more than six hours and not being granted permission to go into Gemlik, Anatolia said.
Ocalan has been in solitary confinement on a prison island in northwestern Turkey since being sentenced to death in 1999 for treason. His sentence was later commuted to life imprisonment.
Kurdish activists and the PKK have urged Ankara to move Ocalan to an ordinary jail from the island of Imrali on the grounds that solitary confinement is inhumane and conditions on the island are affecting Ocalan's health.
Improving Ocalan's prison conditions was one of the demands made by the PKK's political wing, KONGRA-GEL, when it announced a one-month unilateral ceasefire to give Ankara time to improve Kurdish freedoms.
The truce has been brushed aside by the Turkish army.
Some 37,000 people have been killed since 1984 when the rebels first took up arms for self-rule in mainly Kurdish southeast Turkey.