Vote counting started in most areas on Thursday after a delay caused by allegations of irregularities.
It resumed on Saturday after a break on Friday for the start of the Muslim holy month of Ramadan, kicking off for the first time at the regional counting centres of western Herat, eastern Jalalabad and Bamiyan.
"Counting has begun again everywhere - in all eight regional counting centres," said Afghan electoral commission spokesman Aykut Tavsel.
With just 0.7% of estimated total votes counted, US-backed Karzai, the pre-poll favourite, was far ahead with a 72% lead over his rivals.
He was trailed by former education minister Yunus Qanuni with 11%, the Afghan Joint Electoral Management Body said on its website.
In third place with just over 9% was Uzbek regional commander Abd al-Rashid Dustam, and in fourth was Hazara military strongman Muhammad Muhaqiq with 1.6%.
Afghanistan's only female candidate Masuda Jalal was fifth with 1.4% of the votes. The other 13 presidential candidates all had less that 1.1% of the ballots.
Masouda Jalal has 1.4% of the
votes thus far
The initial count included votes from only seven of the country's 34 provinces.
The elections were marred by allegations of fraud and mismanagement after supposedly indelible ink used to mark voters fingers and prevent multiple voting was found to wash off.
An international panel of experts was appointed at the last minute to investigate the complaints, averting a boycott called by disgruntled candidates, some of whom alleged the vote was rigged to favour Karzai, and opening the way for the count to begin.