The night brought some of the worst violence since the trouble began nearly two weeks ago, with police firing tear gas into thousands of people gathered on the square, forcing them to scatter into the surrounding narrow streets. Some of those dispersed were reportedly in office clothes gathered after work, and others included families with children.
A hard core of protesters returned, lighting bonfires and throwing stones at police, before being targeted by tear gas and water cannon.
By dawn the square was largely deserted, save for the wreckage from bulldozed barricades, and taxis crossed it for the first time since the protests started.
Several hundred still remained in an encampment of tents in the adjacent Gezi Park, however.
The Turkish prime minister, Tayyip Erdogan, who has repeatedly dismissed the demonstrators as "riff-raff", was expected to meet a grouping of public figures about the protests today. In the fighting talk that first endeared him to voters 10 years ago, he said yesterday he would not "kneel" before the protesters and that "this Tayyip Erdogan won't change".
The United States, which has held up Erdogan's Turkey in the past as an example of Muslim democracy that could benefit other countries in the Middle East, expressed concern about events in Turkey and urged dialogue between government and protesters.
"We believe that Turkey's long-term stability, security and prosperity is best guaranteed by upholding the fundamental freedoms of expression, assembly and association, and a free independent media," White House spokeswoman Caitlin Hayden said.
Erdogan, though, has increasingly accused foreign forces and international media and market speculators of stoking conflict and trying to undermine the economy of the only largely Muslim Nato state.
He has also exerted strong pressure on the media, seven newspapers last week carrying the identical headline citing Erdogan as saying he, not the protesters, guaranteed democracy.
"We will continue our measures in an unremitting manner, whether day or night, until marginal elements are cleared and the square is open to the people," Istanbul Governor Huseyin Avni Mutlu declared on television on last night.
Police were less in evidence by the morning and it was not clear if protesters would return in the course of the day, as they have previously.
A fierce crackdown on initial protests against planned redevelopment of Gezi Park, a leafy corner of Taksim, triggered the wider protests, drawing in a broad alliance of secularists, nationalists, professional workers, unionists and students - some of whom would never before have considered sharing a political platform.
Erdogan argues that the broader mass of people are at best the unwitting tools of political extremists and terrorists and points to his 50 percent vote in the last of three successive electoral victories for his political authority.
His critics, some of whom who say conservative religious elements have won out over centrist reformers in his AK Party, accuse him an increasingly authoritarian conduct and of inflaming the crisis with unyielding talk.
Some charge that his politics are too often shaped by a religious agenda, with the introduction of alcohol restrictions and comments suggesting he favours a traditionalist role for women.
For his part, Erdogan has complained of the contempt he feels secularist leaders have shown in the past for religious sentiments, excluding women with head scarves from universities. He has accused protesters of attacking women in headscarves and of desecrating mosques by bringing in beer.
"There's no room for dialogue when there's ongoing violence," said Mucella Yapici of the Taksim Solidarity Platform, a core group behind the Gezi Park campaign.
Gezi Park has been turned into a ramshackle settlement of tents by leftists, environmentalists, liberals, students and professionals who see a plan to develop one of the few green spaces in Istanbul as symptomatic of an overbearing government.
Erdogan swept to power in 2002 after forging his AK Party from an alliance of centrist reformers and nationalists as well as remnants of Islamist parties banned in the past by secular authorities. Denying any plans to subvert Turkey's secular order, he set about deep-reaching social reforms.
He broke the political power of an army that had toppled four governments over four decades, including Turkey's first Islamist-led government with which he was associated. He also opened talks with the European Union, introduced some social reforms and sought to negotiate and end to a long-running Kurdish rebellion.
What is notably absent during this crisis is the speculation of a military coup that has in the past accompanied social unrest - some tribute to Erdogan's reforms. Army power is broken. Nor though does there seem to be any political alternative to Erdogan who faces a weak opposition in parliament and fragmented groups on the streets.
"They say the prime minister is rough. So what was going to happen here? Were we going to kneel down in front of these (people)?" Erdogan said after the action to clear the square began on Tuesday morning.
"If you call this roughness, I'm sorry, but this Tayyip Erdogan won't change," he told a meeting of his AK party's parliamentary group.
The unrest has knocked investor confidence in a country that has boomed under Erdogan. The lira, already suffering from wider market turmoil, fell yesterday to its weakest level against its dollar/euro basket since October 2011.
The cost of insuring Turkish debt against default rose to its highest in 10 months, although it remained far from crisis levels.
Turkey's Medical Association said that as of late Monday, 4,947 people had sought treatment in hospitals and voluntary infirmaries for injuries, ranging from cuts and burns to breathing difficulties from tear gas inhalation, since the unrest began more than 10 days ago. Three people have died.
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