Afghan officials said more than seven million people voted, a higher than expected turnout of 52 per cent based on an estimated electorate of 13.5 million voters.
But fraud allegations were likely from both campaign teams after the election, and a close count could lead to a contested result as the country undergoes its first democratic transfer of power.
The election will decide whether former foreign minister Abdullah Abdullah or ex-World Bank economist Ashraf Ghani leads the country into a new era of declining international military and civilian assistance.
Polling day saw no major attacks in cities, but at least 150 other incidents including a Taliban rocket that hit a house near a polling station in the eastern province of Khost, killing five members of the same family.
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"Eleven police, 15 ANA (Afghanistan National Army) and 20 civilians were martyred," Interior Minister Omar Daudzai told reporters, adding that about 60 militants were also killed in fighting.
"Election security was better than the first round despite level of threats being higher," he said. "People voted to reject the militants. There were some casualties on our side, but the enemy has failed."
President Hamid Karzai is due to step down after ruling Afghanistan since 2001, when a US-led offensive ousted the austere Taliban regime for sheltering Al-Qaeda militants behind the 9/11 attacks.
"We are very proud to be choosing our favourite candidate," he said after voting. "Today Afghanistan goes from a transition period towards long-lasting peace."
A smooth handover would be a major achievement for the international effort to establish a functioning state after the depredations of the Taliban era.