Officials involved in flawed Afghan elections are being removed ahead of next month's run-off, the UN has said.
The second round, between Mr Karzai and former Foreign Minister Abdullah Abdullah, has been scheduled for 7 November.
Voters in Afghanistan have been digesting the news that they will be required to cast their votes again. Here are some of their thoughts.
EBRAHIM BAREKZAI, 35, GOVERNMENT WORKER, KABUL
It is clear to all that Mr Karzai is our legitimate president after the elections on 20 August.
If the US and other Western countries want a peaceful and stable Afghanistan, they should respect the votes of the poor Afghan people.
My request to the international community is - don't interfere in the elections, otherwise the consequences will be very bad for Afghans and for our international friends.
I am sure that President Karzai will win in the second round - but it's going to be a waste of time and money in such a poor and unstable country.
This is Afghanistan, not Germany or the UK. Democracy is new here.
There is no guarantee that there won't be fraud during the run-off. Only one thing is certain - the Taliban will benefit from this situation.
AIMAL ABDUL GHAFAR, 32, COMPANY WORKER, KUNDUZ
The people of Afghanistan are not allowed to make decisions anymore. It's Western countries and America in particular who make the decisions in Afghanistan.
They are not here to bring peace, but chaos.
There was some fraud, I am not rejecting that and it is a concern. Once they establish who committed the fraud, that person should be disqualified for ever. They should not be allowed to run in an election again, as they might do it again.
You can't run for government office if you are guilty of corruption and fraud. There should be new requirements for entry into the election race and we should have new candidates.
Otherwise the problems surrounding the election on 20 August will exist during the run-off. This is disrespectful for those who dared to vote during a difficult security situation.
There is lots of Taliban activity in the whole province of Kunduz, where I live. There are explosions and suicide bombings all the time.
There was fighting in the main city of Kunduz and there were rocket attacks on election day. The highway from Kunduz to Baghlan has also been in the control of militants.
Going to the polls was a big risk. Many preferred to stay at home and only a few went out to vote.
I took the plane to Kabul so I could vote there and I waited there for the ink on my finger to fade away before I returned to Kunduz. The Taliban gave a clear message as to what they would do with those who voted.
People took a risk to vote and then their votes were dismissed. I am not going to vote again.
ABDUL MALIK NIAZI, DIRECTOR, KABUL
This is bad news for Afghanistan. We, Afghans, risked our lives in order to elect our president and now, due to foreign interference, we have to do it again.
The international coalition blames our government for everything from the day they put their soldiers on our land. Decisions are made from outside Afghanistan, and I am worried that we'll have a president we didn't want imposed on us.
I doubt that the ECC findings are correct. I do accept that there was fraud, but there should have been some kind of compromise. Why did they have to annul 30% of the votes for Karzai? They could have said only 10 or 20. But I think they wanted to make sure that he didn't get the 50% he needed to win.
The same will happen in the second round, so it doesn't really solve the problem.
It's not going to be possible to hold the elections in two weeks. The weather is changing, it's getting cold and it's going to be very difficult for people to go out and vote. The timing is bad and the turnout will be very low.
The security situation also worries me. This is not Europe - it's Afghanistan.
MUZAFAR ALI, 28, OFFICE WORKER, DAIKUNDI, HAZARAJAT
Unfortunately the decision for a run-off has come too late. The government backed election commission has (unintentionally and unwillingly) dented Karzai's chance of retaining his post for a second time by delaying a run-off, because upcoming severe cold weather in most parts of the country will prevent people from voting.
This is the first Afghan led election and it was overshadowed by irregularities in the process. A run-off means the next Afghan election will need more intense involvement of foreign observers during the process.
The Taliban's presence and anti-government propaganda has intensified in many areas. People are concerned about this matter, especially in many parts of Taliban ruled Gezab district which borders peaceful Dai Kundi province.
In the places where the Taliban used to have surprise visits in Gezab they now have a permanent presence. They thoroughly search incoming and outgoing vehicles and passengers.
To some extent the run-off can wash off the bad reputation of the Independent Election Commission (IEC) of Afghanistan.
I am quite hopeful that the run-off will bring a glimmer of hope for Afghans who are currently disappointed. The IEC also needs a major overhaul to prevent such irregularities in future elections.
If IEC officers and authorities were responsible for fraud they should not only be sacked from their position but should also be investigated and put in prison if they are found guilty. Afghans have to pay a huge price for such irregularities in elections. It will take time to fully recover from current situation created by the current political dilemma.
SEEMA GHANI, ORPHANAGE HEAD, KABUL
The news that there will be a run-off is no surprise. As soon as I knew there would be a percentage, I assumed there would either be a run-off or some sort of a deal made by the international community with the current president, to make him agree some promises for the future.
Projects are at a standstill, international and national NGOs, companies and organisations are not making decisions. My personal experience is that my own company is at a loss because our services are based on the international companies running projects and nothing is happening.
The house I am renting has a high price because the house prices rose for Karzai and Abdullah's campaign houses. So as long as they pay the landlords, ordinary people have to suffer. Also I am a member of a newly established commission for women (Afghan Women Independent Economic Commission) and we cannot register because in the absence of a president no-one else can sign.
Ordinary people are talking about leaving the country if there are riots. The US army is no longer planning to send troops.
So the lives of people in this country are at a standstill because Karzai and Abdullah and their followers are corrupt. I will not waste my time in voting for them. They don't deserve it and they are not good leaders for this country. I would have voted for a coalition of many leaders coming together but not for these two as individuals.
Any next government doesn't have the legitimacy we expected before the first round. The level of fraud is embarrassing. I can never trust a government led by either of these two people anymore. I just hope we can survive the next five years and during this period I hope we can train some real leaders.
BASEER FARAHI, 25, STUDENT, KABUL
I am 100 percent sure that more than 60 percent of people will not go to vote, because they know that there will be even more fraud. Another factor is the Taliban who say if they find anyone with ink on their finger, his or her hand will be cut off.
Now people are asking whether going to vote is worth the risk. If we knew that we were voting for a real government then the risk would be worth it.
People are not buying anything, no-one is investing their money in business. Everyone is waiting to see what will happen next. What will the security by like? Where will they go if anything goes wrong?
We need a change in our entire government. We need real people who should work for this country.
Our current government is hopeless, especially Mr. Karzi. I won't call him president because he does not deserve it. Whatever we are facing today it is because of him. He has put the wrong people in to positions of governors, chiefs of polices and even ministers.
HARIS, ASST. PROFESSOR OF OPTHALMOLOGY, JALALABAD
I think a run-off will be a waste of the available resources. The local and international measures put in place cannot be improved just by changing a few afghans at the election stations nor can we improve the election process. The fraud will occur again and again if we conduct the election even 100 times.
I accept that there were some irregularities and fraud but not to the extent that disturbs the legitimacy of the election and mandates a second round. I think in a country such as Afghanistan this amount of fraud and irregularities are inevitable; particularly in a country with a young democracy such as Afghanistan. I am not in the favour of second round of election.
I am not so sure that this round is the real aspiration of afghan people. I will never vote again because it will waste my time.