Fraud allegations were likely from both campaign teams after the run-off vote, and a close count could lead to a contested result as the country undergoes its first democratic transfer of power.
Despite being mainly peaceful, polling day saw at least 150 minor attacks, 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.
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.
He admitted there had also been problems with ballot paper shortages, but said that affected polling stations had been re-supplied.
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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.
A smooth handover would be a major achievement for the international effort to establish a functioning state after the depredations of the Taliban era.
"We are very proud to be choosing our favourite candidate," Karzai said after voting. "Today Afghanistan goes from a transition period toward long-lasting peace."
"As we promised, the security was better and we had better planning," said interior minister Omar Daudzai on Saturday. "The enemy's attacks have had very little impact."
Daudzai said the day was proof that the security forces, who have been trained by the US-led military coalition, were able to protect the country as all NATO-lead combat troops exit Afghanistan this year.
Both candidates cast their ballots in Kabul before dipping a finger in ink to register that they had voted.