The election commission said on Sunday that Karzai had polled 61.6% of the estimated 8.3% of votes counted.
In second place with 17.6% was former education minister Yunus Qanuni, the Joint Electoral Management Body said in a statement.
In third place with 11.4% was Uzbek regional commander Abd al-Rashid Dostum, while Hazara commander Muhammad Muhaqiq was in fourth with 3%.
In seventh place was the only woman out of the 18 presidential candidates - Masuda Jalal - who had garnered 1% of the vote.
President Karzai is widely expected to maintain his strong lead in the coming days.
He commands strong support from the country's majority Pashtun community who live mainly in the south and southeast.
The elections passed off without
the expected surge in violence
In the northern Panjshir valley, Tajik Qanuni won 95% of the vote so far, reflecting how voting has broken up along ethnic lines.
Afghanistan's election passed off without major violence but was hit by allegations of fraud and mismanagement.
Opposition candidates alleged the vote had been rigged to favour Karzai.
An international panel was appointed at the last minute to investigate their complaints and head off a threatened boycott of the 9 October polls.
Some 686,447 of an estimated seven million votes have so far been counted.