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.
"The voting has gone well and as planned. As you see, the turnout has been large," said Independent Election Commission chief Ahmad Yusuf Nuristani.
He admitted there had also been problems with ballot paper shortages, but said that affected polling stations had been re-supplied.
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."
Security and jobs
In the first-round vote in April, the insurgents also failed to launch a high-profile attack and voter turnout was more than 50 percent.
"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.
"We do not want even one fraudulent vote for us," Abdullah told reporters, while Ghani said via Twitter: "We ask everyone to prevent, avoid and discourage people from rigging."
On the eve of the run-off, UN head of mission Jan Kubis issued a stark warning to candidates' supporters not to resort to the ballot-box stuffing that marred the 2009 election when Karzai retained power.
The two candidates came top of an eight-man field in the April election, triggering the run-off as neither reached the 50% threshold needed for outright victory.
Abdullah secured 45 percent of the vote with Ghani on 31.6%, after investigations into fraud claims from both sides.
On the campaign trail, they offered similar pledges to tackle rampant corruption, build much-needed infrastructure and protect citizens from violence.
"I want someone who can improve our economy, create jobs and improve our lives," said Janat Gul, 45, a shopkeeper voting in Kabul.
"If the economy is good there will be no insurgency, everyone will be busy working, not fighting."
Harsh terrain and poor roads make holding an Afghan election a logistical challenge, with thousands of donkeys used to transport ballot boxes to remote villages.
Counting the ballot will take weeks. The preliminary result is due on July 2 and a final result on July 22.
Ahead of the vote, the Taliban said that polling booths would be targeted by "non-stop" assaults.
"The Americans want to impose their stooges on the people," the insurgents said.
The search for peace
Karzai, who is constitutionally barred from a third term in office, has fulfilled his pledge not to interfere in the election -- in public at least -- though he is tipped to retain influence after handing over power.
His relationship with the US soured badly, and the next president is likely to reset ties by signing a long-delayed pact for some US troops to remain on a training and counter-terrorism mission after this year.
Last month President Barack Obama said that if the pact is signed, 9,800 of the 32,000-strong US deployment would stay in 2015.
The US-led NATO military mission was in a "support role" on Saturday, ready to assist if requested by Afghan authorities.
Priorities for the incoming president will be to stabilise the faltering economy as aid falls, and a fresh attempt to bring peace after decades of war by exploring peace talks with the Taliban.
Ethnic friction is also a concern as Abdullah's support is based among the Tajik minority and other northern tribes, while Ghani is a Pashtun -- Afghanistan's largest ethnic group, which is strongest in the Taliban heartlands of the south and east.