Afghan officials are estimating that the turnout in a presidential run-off was about 60%, and nearly 50 people have been killed in attacks nationwide.
Independent Election Commission chairman Ahmad Yousuf Nouristani said more than 7 million Afghans voted in the election to choose a leader to replace Hamid Karzai. There were about 12 million eligible voters.
Interior Minister Mohammad Umar Daudzai also said dozens of people were killed, including 20 civilians, 15 army soldiers and 11 policemen, but the overall voting was largely peaceful.
The two men spoke at a news conference after polls closed.
The presidential hopefuls - former foreign minister Abdullah Abdullah and ex-World Bank official and former finance minister Ashraf Ghani Ahmadzai - differ more in personality than in policy.
Both have promised to sign a long-delayed security pact with the United States. That would allow nearly 10,000 American troops to remain in the country for two more years to conduct counterterrorism operations and continue training and advising the ill-prepared Afghan army and police.
“I voted today for my future, because it is still not clear – the country is at war and corruption is everywhere and security is terrible. I want the next president to bring security above all and jobs,” said 20-year-old Marya Nazami, who voted for Mr Ahmadzai.
The Taliban intensified attacks ahead of the vote and warned people to stay away from the polls, but the Islamic militants failed to disrupt the first round on April 5 and security forces launched a massive operation.
Troops frisked voters before allowing them into polling stations and erected checkpoints around the capital of Kabul to search cars for explosives or other weapons. Trucks also were banned from the city.
Still, the militants made their presence known. A series of rockets slammed into areas in the eastern Khost province, near the Pakistani border, killing six civilians and wounding eight, according to provincial government spokesman Mubarez Mohammad Zadran. Elsewhere in the east, a mortar shell killed two other civilians and wounded three in Logar province. Several other explosions were reported in Kabul and elsewhere.
In all, nearly 50 people were killed in attacks nationwide but authorities said they had foiled numerous insurgent plots and the overall voting was relatively peaceful.
Official preliminary results are to be announced on July 2 but Mr Nouristani said his panel planned to release partial results in coming weeks.
Many voters said they were eager to get the bilateral security agreement signed after watching Islamic extremists seize large sections of Iraq nearly three years after US troops withdrew from that country. Iraq’s Shiite-led government had discussed with the Americans the possibility of a residual US force but the two sides were unable to reach an agreement.
President Hamid Karzai, who has grown increasingly alienated from his one-time US allies during his two terms in office, has refused to sign the pact.
“Iraq is burning,” Abbas Razaye, a 36-year-old shopkeeper, said after voting in a mosque in western Kabul. “We need the foreign troops for the time being. Otherwise our history of civil war will repeat itself and Afghanistan will deteriorate even more than Iraq.”
Sayed Qayyum, 58, agreed the pact should be signed. “I am afraid if it isn’t signed then Afghanistan will face the same fate as Iraq,” he said.
Mr Abdullah and Mr Ahmadzai were facing off after none of the eight candidates in the first round won the majority needed to avoid a second round. Mr Abdullah emerged as the front-runner after he garnered 45% of votes in the initial balloting. Mr Ahmadzai was second with 31.6%.
The two have since campaigned as much for the support from their six former rivals as from Afghans themselves.
Abdul Hakim, a 25-year-old businessman, said he voted for Mr Abdullah in both elections, and he has high expectations.
“I want Abdullah to remove corruption and poppy cultivation and bring security. He should definitely sign the BSA,” he said. “Afghanistan has no economy. Afghanistan has very bad security.”
With Mr Karzai out of the race, Mr Ahmadzai has gained the support of many Pashtuns who voted against him five years ago, particularly in the Taliban heartland in southern Afghanistan.
“According to our will, Ashraf Ghani is the best candidate and the rightful leader of our country,” said Abdul Saboor Zamaria, a 30-year-old working for a nongovernmental organisation in the southern city of Kandahar. “If Abdullah Abdullah is made our leader more mistrust and rage will spread in our country and violence will keep increasing day by day.”