The count was put on hold for a day on Friday as Muslims marked the start of the fasting month of Ramadan.
Election spokeswoman Silvana Puizina said counting had resumed at 9 a.m. in the capital, Kabul, and in other counting centers across the country.
Earlier, however, a preacher at Kabul's main mosque, Mullah Obeid-ul Rahman warned that Afghans won't stand for arrogance in whomever wins.
Karzai, who has led this predominantly Muslim country since the US-led forces ousted the Taliban regime in late 2001, is widely expected to win the October nine vote.
The UN-backed election, which cost about USD 200 million to stage, has generated huge interest among Afghans, who are aching for peace after conflicts spanning the Soviet occupation of the 1980s, a murderous civil war in the early 1990s and then the Taliban's tyrannical rule.