Electoral officials rejected the candidates' call to abandon the rest of the balloting, saying it would rob millions of voters of their chance to cast ballots and that they would rule later on the legitimacy of the election.
"Halting the vote at this stage is unjustified and would deny these people their right to vote," said Ray Kennedy, the vice chairman of the joint U.N.-Afghan panel overseeing the election. "There have been some technical problems but overall it has been safe and orderly."
Karzai said the fate of the vote was in the hands of the electoral body, but he added that in his view "the election was free and fair ... it is very legitimate."
"Who is more important, these 15 candidates, or the millions of people who turned out today to vote," Karzai said. "Both myself and all these 15 candidates should respect our people — because in the dust and snow and rain, they waited for hours and hours to vote."
The boycott cast a pall over what had been a joyous day in Afghanistan.
Millions of Afghan voters braved threats of Taliban violence to cram polling stations throughout this ethnically diverse nation, in an election aimed at bringing peace and prosperity to a country nearly ruined by more than two decades of war.
It also was a blow to the international community, which spent just under $200 million staging the vote. At least 12 election workers, and dozens of Afghan security forces, died in the past few months as the nation geared up for the vote.
The opposition candidates, meeting at the house of Uzbek candidate Abdul Satar Sirat, signed a petition saying they would not recognize the results of the vote, saying glitches with the ink used to mark voters' thumbs opened the way for widespread fraud.
Election officials said workers at some voting stations mistakenly swapped the permanent ink meant to mark thumbs with normal ink meant for ballots, but insisted the problem was caught quickly.
Sirat, an ex-aide to Afghanistan's last king and a minor candidate expected to poll in the low single-digits, said all of the 15 candidates still in the race against Karzai agreed to the boycott.
"Today's election is not a legitimate election. It should be stopped and we don't recognize the results," Sirat said. "This vote is a fraud."
U.S. Ambassador Zalmay Khalilzad arrived at the house later to meet with Sirat, making no comment other than to say he was there "only to help."
Khalilzad, a naturalized U.S. citizen born in Afghanistan, has been widely criticized for perceived favoritism for Karzai, and is seen as a puppet-master by many Afghans. Several Afghans gathered outside the house joked that a resolution to the crisis was near because "the big man has arrived."
Kennedy said it could take time for the electoral body to reach a decision on the vote's legitimacy. U.N. spokesman Manoel de Almeida e Silva had said earlier that the problems were not as pervasive as the opposition claimed.
"I don't think we can lose sight of the perspective," the U.N. spokesman said. "There are 23,000 polling stations in the country. We do not have indications it (the ink problem) was to a great extent."
Karzai's spokesman, Khaleeq Ahmed, said the president planned a news conference later in the day.
The European Union and the Organization for Security and Cooperation in Europe sent observer missions, but neither said it planned to pass judgment on the fairness of the process, saying it would not be appropriate to try to hold Afghanistan to international standards. A small U.S. observer team also was monitoring the vote. None had an immediate comment on the controversy.
Initial results from the election — in any case — had not been expected until late Sunday or early Monday, but anything approaching a full count could take as much as two weeks.
About 10.5 million registration cards were handed out ahead of the election, a staggering number that U.N. and Afghan officials say was inflated by widespread double registration.
Human rights groups say some people obtained four or five voter cards, thinking they would be able to use them to receive humanitarian aid. Vote organizers had argued that the indelible ink would prevent people from voting twice.
Massooda Jalal, the only female candidate, said she joined the boycott petition after getting complaints from her constituents. "The ink that is being used can be rubbed off in a minute. Voters can vote 10 times!" she said.
Another candidate, ethnic Tajik newspaper editor Hafiz Mansoor, also complained of fraud. "Very easily they can erase the ink," he said. "This is a trick that is designed to clear the way for cheating."
The boycott announcement put an end to what had been an optimistic, peaceful start to this nation's first-ever experiment with democracy.
Voters queued for hours outside polling stations in bombed-out schools, blue-domed mosques and bullet-pocked hospitals to cast ballots, while more than 100,000 soldiers, police, U.S. troops and other security forces were deployed to thwart attacks.
Heightened security measures appeared to work, despite plenty of signs Taliban rebels were trying to disrupt the polls.
On Friday, a bomb-sniffing dog discovered a fuel-truck rigged with anti-tank mines and laden with 40,000 liters (10,000 gallons) of gasoline that three Pakistanis planned to detonate in the southern city of Kandahar, said Col. Ishaq Paiman, the Defense Ministry deputy spokesman.
The blast would have killed hundreds and "derailed" balloting in the south, he said.
The election offered a stark contrast in a nation that has endured many forms of imposed rule in the past 30 years — among them monarchy, Soviet occupation, warlord fiefdoms and the repressive Taliban theocracy ousted by the U.S.-led invasion following the Sept. 11, 2001, terrorist attacks.
"I came here to vote so we can have democracy and stability and peace in Afghanistan," said Aziz Ullah, a 19-year-old Kabul shopkeeper. "There used to only be a transfer of power by force or killing."