Polling centers in cities and villages opened at 7:00 a.m. local time (0230 GMT) and continued till 5:00 p.m. local time (1230 GMT) in the country's 34 provinces, officials with the election commission said.
The voting process initially was to end at 3:00 p.m. local time but extended for two more hours to enable the voters to use their franchise, head of the election commission Hawa Alam Nuristani told reporters.
It is the fourth presidential election in Afghanistan since 2001, when the Taliban regime was ousted from power.
Over 9.4 million eligible voters, 35 percent of them women, registered to cast their votes in Saturday's polling.
Fourteen out of the 18 registered contesters are vying for the presidency with a five-year term and among the candidates are sitting President Mohammad Ashraf Ghani and government Chief Executive Abdullah Abdullah. Four candidates have withdrawn from the race in favor of one candidate.
Security remains the biggest challenge for the election. The Taliban outfit has vowed to disrupt the election process. A number of security incidents have been reported from across the country.
Meanwhile, the security forces' fighting planes in crackdowns on militants have killed 25 armed insurgents in the northern Balkh and eastern Logar provinces since Friday to ensure security for the election process.
Taliban attacks have also claimed at least four lives and wounded eight others in the northern Kunduz city and wounded 15 others in the southern Kandahar city on Saturday.
The militants' attacks and possible fraud have remained top concerns of the voters.
"I don't like to be killed in a suicide attack or bombing at a polling center for voting. I want to remain alive and continue my education to serve my country in future," said a university student Bushra Parnian, 20, in talks with Xinhua.
Fearing possible fraud in the voting process, many voters have complained that the biometric devices in some polling centers were out of order which undermines the polling transparency.
"I went to a polling center in Aziz Afghan Secondary School in Kabul Police District 10 and voted for my favorite candidate with the hope that my single vote could bring positive change in my life," a Kabul resident, Hamidullah Nayel, told Xinhua.
However, he expressed doubt over the fairness of the voting process, saying, "If the fraud-marred 2014 presidential election repeated, the country may plunge to crisis."
Afghanistan's previous presidential election was held in April 2014 but months' delay in announcing the result almost took the country to the edge of civil war and finally led to formation of National Unity Government with the mediation of former U.S. Secretary of State John Kerry.
The election body's chief Nuristani has dismissed all security problems and possible fraud for Saturday's voting, saying all necessary measures have been taken to provide security for the voters and ensure transparency in the polls.