Many protesters regrouped in nearby Gezi Park, where unrest continued into Wednesday morning.
At dawn, bulldozers moved into Taksim Square to clear away debris, barricades and makeshift shelters.
Protests began 13 days ago over the redevelopment of Gezi Park.
They then widened, with demonstrators accusing Prime Minister Recep Tayyip Erdogan of becoming increasingly authoritarian and trying to impose conservative Islamic values on a secular state.
Mr Erdogan has offered to hold talks with protest organisers on Wednesday but correspondents say it is unclear whether the meeting will still take place in light of the clashes.