Turnout was strong in the capital Kiev and the west but across swathes of the rebel-controlled industrial east, most polling stations remained closed.
"Ukraine is now another country so I don't see why we should take part in this election," said one woman in the rebel-held city of Donetsk who gave her name as Elisabeta. "It doesn't matter what the result is, it doesn't concern us."
The West regards the vote as a crucial step in preventing Ukraine from disintegrating further after Russia seized the Black Sea peninsula of Crimea in March in retaliation for the ouster of pro-Kremlin president Viktor Yanukovych.
"I hope this election will finally bring peace to Ukraine," said 38-year-old businessman Oleg as he voted in the western nationalist bastion of Lviv near the Polish border.
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But in the Donetsk region alone, where rebels declared independence earlier this month in defiance of Kiev, only 426 out of 2,430 polling stations were open, and none in the main city.
Even before polling day, election officials had reported numerous cases of intimidation and attacks on polling centres and rebels threatened they would disrupt the vote "by force if necessary".
President Vladimir Putin - authorised by parliament to invade Ukraine if necessary to "protect" ethnic Russians - had appeared to make a major concession Friday by saying he was ready to work with the new Kiev team.
"We understand that the people of Ukraine want their country to emerge from this crisis. We will treat their choice with respect," he said.
Ukraine has mobilised more than 82,000 police and 17,500 volunteers to ensure security for the vote, being overseen by 1,200 international monitors.