Police began dismantling the tents that protesters had put up in the park.
The move came hours after PM Recep Tayyip Erdogan warned protesters to evacuate the area ahead of a rally by his AK party on Sunday.
Plans to redevelop the park sparked a wave of broader anti-government unrest and protesters had vowed to stay there until their demands were met.
In a show of overwhelming force, police advanced into the park wearing riot shields and gas marks.
Most of the protesters left of their own accord to avoid getting hurt, with some regrouping in nearby streets.
Local residents took to their balconies or leant out of windows banging pots and pans, while car drivers sounded their horns in support of the protesters, Reuters news agency reports.
Some of the protesters were reportedly receiving medical attention, several of them retreating into a nearby hotel.
Istanbul Governor Huseyin Avni Mutlu said 29 people had been injured in the raid, but none seriously.
Huseyin Avni Mutlu said only “marginal groups” had remained in the park.
“I won’t give up,” protester May Elbi told AFP.
“We’re angry, this is not over. The world has seen that together, we can stand up to Tayyip.”
There have been reports of fresh confrontations in Istanbul after the clearing of the park, with police again using tear gas to disperse protesters.
In the capital Ankara, thousands of people came out onto the streets to chant anti-government slogans.
Earlier, in a speech in Ankara, Recep Tayyip Erdogan told tens of thousands of AK party supporters: “If Taksim Square is not evacuated, this country’s security forces will know how to evacuate it.”
“Staying there [in Gezi Park] makes no sense anymore as the matter is now in the hands of the courts,” he told tens of thousands of cheering supporters.
“Nobody can intimidate us. We take no orders or instruction from anyone but God,” the prime minister added.
He also dismissed the wave of demonstrations as part of an organized plot against him.
One protest group responded to Recep Tayyip Erdogan’s speech by calling for another mass rally in Taksim Square. Istanbul is also set to host an AK party rally on Sunday,
On May 31, a crackdown on environmentalists in Gezi Park provoked protests across Turkey against the police’s actions and against Recep Tayyip Erdogan’s government.
On Saturday, the protesters vowed to stay there, despite a promise by Recep Tayyip Erdogan to halt the development plan for the park until a court ruling on the issue.
Last month, an Istanbul court issued an initial injunction against the plan to cut down trees in the park to make way for a shopping centre and replica 18th-Century military barracks. The government has appealed against the ruling.
Recep Tayyip Erdogan’s offer was presented as a major concession. But after discussions in Gezi Park on Friday night, the protesters said their movement was more than just a conservation protest and vowed to stay on.
Five people have died and thousands have been injured since the protests began.
Demonstrators have accused Recep Tayyip Erdogan’s government of becoming increasingly authoritarian and of trying to impose conservative Islamic values on a secular state.
The police crackdown on protesters in Istanbul, Ankara, and other towns and cities has drawn international concern, especially from Europe.
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