But thousands of allegations of fraud are still being investigated amid growing international concern, particularly among those nations whose troops are currently fighting the Taliban in Afghanistan.
And questions are being asked about how the such a flawed result was able to happen.
The system had an inbuilt potential for fraud as the Independent Election Commission was responsible for all three of the processes in the election - registering voters, running the poll and carrying out the count.
Registration problems
Eight years after the fall of the Taliban, Afghanistan is still a long way from having a national ID card system, or any other agreed way of registering citizens.
Millions of dollars have been spent on pilot schemes, but none has been adopted amid political infighting both within the international community and between Afghan ministries.
So the Election Commission started afresh to build an electoral register in October last year.
They did not carry out any biometric tests such as iris scans or fingerprint checks - although these are foolproof and can be cost-effective.
A guard stands by ballot boxes at the Independent Election Commission
Irregularities with ballot boxes were noticed on polling day
Afghanistan pioneered iris recognition in the field in 2002 in order to process hundreds of thousands of returning refugees, but this knowledge was not built on, and the Election Commission registered voters by asking them to turn up in person.
An outside body that looked into the process - the Free and Fair Election Foundation of Afghanistan - found widespread irregularity in the process.
Violations included the registration of underage voters, registration of people from a list who did not attend in person, and lack of impartiality.
For example, in Lashkar Gah, the main headquarters of the British army in Helmand province, a local teacher was alleged to have had undue influence over who was registered.
In the remote and poor central province of Oruzgan warlords were seen to control the registration process.
Manipulating votes
This made the manipulation of the voting process far easier to do.
Irregularities witnessed by observers on polling day included ballot boxes that were already full as the polls opened, a higher number of votes than voters registered, and districts where there were an even number of votes, usually 500, in each ballot box.
But the evidence that suggested to losing candidates that the count itself was not impartial came when it emerged that votes had been counted from polling stations that were known to have been closed on 20 August - for security or other reasons.
That is what prompted the leading challenger Abdullah Abdullah to criticise the counting process in a strongly worded interview for the BBC on Thursday, in which he said that the Independent Election Commission was not independent, and that it was being manipulated to keep a "mafia-type, narco state" in power.
"As long as it takes," he said, it is important that the "election is not decided by fraud."
Afghan election candidate Abdullah Abdullah
Candidate Abdullah Abdullah has been critical of the voting process
The Independent Election Commission is investigating more than 700 complaints. Some of these refer to just one polling station, but others cross entire districts.
Meanwhile, the Electoral Complaints Commission, an oversight body with a majority of internationally appointed members, has ordered an audit of the whole election.
It wants a recount where there was a 100% turnout or more than 95% of votes for one candidate. This could take up to two months.
But in a sign of growing tension between the Afghan-led Independent Election Commission, and the international-led Electoral Complaints Commission, the order was rejected when initially sent earlier in the week, in a row over translation.
The Complaints Commission has widespread powers and has since flexed its muscles further, ordering that votes should be annulled from more than 70 polling stations in Ghazni, Paktika and Kandahar.
This is a dreadful outcome for a country facing a worsening insurgency.
International interest
A reliable independent observer, ICOS, assessed this week that the Taliban now have a presence in more than 80% of the country, up from 54% two years ago.
The international forces who are trying to secure stability have little appetite for another election, and opinion polls in Europe and the US show the public are losing patience for the war.
The outcome of this election is that President Karzai remains in power for now, with his authority substantially weakened, tainted by claims of corruption - and facing a strong challenge over his legitimacy, particularly in the Tajik heartland of the northeast, the headquarters of the northern alliance forces that drove the Taliban from power with US assistance in 2001.
And he faces a particular problem in Balkh and Jawzjan in the north, where the ex-warlord General Abdul Rashid Dostam campaigned for him in return for favours that President Karzai may not be strong enough to deliver.
As the recount begins, in a country where people still follow the lead of tribal elders, a very high margin for one candidate may not imply fraud, but it is at least an indicator worth examining.
The one politician to defy the tribal vote-banks was Ramazan Basherdost, the only candidate other than Karzai or Abdullah to win a significant number of votes.
He campaigned on the single platform of anti-corruption, and with no party machine, came a creditable third - signalling that there are many people in Afghanistan who are prepared to hope for honesty and vote against the divisions of the past.
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