Election authorities refused to halt the voting despite the boycott.
"The vote will continue because halting the vote at this stage is unjustified and would deny these people their right to vote," said the vice-chairman of the joint UN-Afghan electoral body, Ray Kennedy. "There have been some technical problems but overall it has been safe and orderly."
Supporters of Yunus Qanooni, the main challenger to President Hamid Karzai, alleged that voting booths in areas where their leader had support were not opened in time.
The boycott followed complaints of fraud over the use of indelible ink that candidates say was meant to ensure people voted only once, said the Arabic news channel Al Jazeera.
The opposition candidates, who met at the house of Uzbek candidate Abdul Satar Sirat, released a signed petition saying that they would not participate in the vote because the mix-ups with the ink used to mark voters' thumbs opened the way for widespread fraud.
"Today's election is not a legitimate election. It should be stopped and we don't recognize the results," said Sirat, an ex-aide to Afghanistan's last king.
Sirat said that every one of the 15 candidates agreed to boycott the poll, and many other candidates at the meeting joined them. "We are not taking part today," Sirat said. "This vote is a fraud."
According to Al Jazeera, the ink problem was reported at many voting centers in Kabul and the northern city of Mazar-e-Sharif, where voters said that they could easily rub off the ink and that they could not vote more than once.
Election officials said the the problem occurred at a few polling stations where workers mistakenly used normal ink meant for ballots to mark people's thumbs.
Similar complaints were reported from northeastern Kunduz and central Baghlan provinces, but in limited numbers, said Farooq Wardak, director of the electoral commission.
Among those boycotting the vote was Massooda Jalal, the only female contestant.
"In the morning I was prepared to vote, but within the past three hours I've received calls from voters that this is not a free and fair election," Al jazeera quoted her as saying.
"The ink that is being used can be rubbed off in a minute. Voters can vote 10 times!"
"Very easily they can erase the ink," said another candidate, Hafiz Mansoor. "This is a trick that is designed to clear the way for cheating."
According to Al Jazeera, the problem is compounded by the fact that many people received more than one registration card by mistake.
"Up to 10.5 million registration cards were distributed ahead of the election, a large number that UN and Afghan officials say was affected by widespread double registration. Human rights groups say some people received four or five voter cards, thinking they would be able to use them to receive humanitarian aid," the Arabic news channel said.
With 5,000 polling places set up across vast stretches of desert and remote mountain bypasses, the final results might not be declared for several days.
But though radical insurgents have killed at least 60 people nationwide since the campaign started September 7, and Karzai and his allies have been attacked three times, there were no major reports of violence Saturday.
"I think the opponents of democracy are back on their heels," said Col. David W. Lamm, chief of staff for the coalition forces in Afghanistan.