World leaders praised the courage of Afghan voters, who cast their ballots in force despite bad weather and the violent campaign of intimidation, and urged patience in the long vote count.
Ahead of the poll there were fears that a repeat of the massive fraud that blighted Karzai's re-election in 2009 would undermine the winner's legitimacy at a testing time for the war-torn country.
There were reports of polling stations in numerous parts of the country running out of voting papers, leaving some people unable to take part, as well as claims of ballot-stuffing.
Zalmai Rassoul, who was regarded before the vote as Karzai's preferred choice, said today that he had made complaints to the ECC, but refused to give details.
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He said he was confident the ECC would address the concerns properly but warned: "Any president elected with fraud will not be accepted by Afghanistan."
Former World Bank economist Ashraf Ghani, who claimed to be in the lead in preliminary results, voiced similar views.
"I would like assure all Afghans, whether they voted for us or not, that we will form an inclusive government that treats all Afghans equally."
Whoever emerges victorious from the lengthy vote-counting and appeals process faces the prospect of fighting the Taliban without the help of US-led combat troops.
There were fears that a disputed result could spark bitterness and recrimination and put the new president in a weak position.
The third leading candidate, Abdullah Abdullah, runner up in 2009's acrimonious poll, said he had also filed complaints.
An estimated seven million people voted, according to the Independent Election Commission (IEC), more than 50 per cent of the electorate -- a huge increase on 2009 when only around a third of those eligible cast ballots.
Preliminary results are due on April 24 and if no candidate secures more than 50 per cent of the vote, a runoff is planned for late May.