The Afghan leader along with other high-ranking officials arrived at Amani High School near the presidential palace at around 7.45 a.m. to cast their vote, Xinhua reported.
Karzai, who is constitutionally barred from running for a third consecutive five-year term, urged all Afghan voters to take part in the election process. "Today is a historic day in Afghanistan. I urge all Afghans to visit the polling centres and cast their votes for a bright future, for a new president and for a new government," Karzai said.
The runoff election will decide whether former foreign minister Abdullah Abdullah or ex-World Bank economist Ashraf Ghani Ahmadzai leads the country into a new era with declining international military and civilian assistance.
Karzai: I urge all Afghans to visit the polling centres and cast their votes
The two entered a runoff after none of the eight candidates obtained an outright victory or more than half of the valid votes in the first round held April 5. According to the final results of the April 5 election, Abdullah secured 45 percent of some 7 million votes, and Ahmadzai won 31.6 percent.
Afghans began voting earlier on Saturday to elect a new president for the next five years in the first transfer of power through polling in the country's history.
The polling began at 7 a.m. and will end at 4 p.m.
More than 12 million eligible voters, 35 percent of them women, are expected to cast their ballots in the one-day election across Afghanistan. The preliminary results of the runoff will be announced July 2 while the final result of the polls will be declared July 22.