Hamid Karzai, the Afghan president, "strongly condemned the attack" in a statement.
"The enemies of Islam and Afghanistan showed their enmity with Islam and the people of Afghanistan by firing rockets into Kabul with no specific target, killing three innocent civilians while asleep in Ramadan," he said.
The latest attack on the capital comes amid increasing concern over fraud in the country's elections.
Noor Mohammed Noor, a spokesman for the Independent Election Commission, said on Sunday that officials had annulled votes from 447 polling stations due to fraud.
He said that as each polling site had about 600-700 ballots, the cancelled votes "could be around 200,000 votes".
The New York Times newspaper reported that Afghans loyal to Karzai set up as many as 800 fictitious polling sites ahead of elections, where no one voted but hundreds of thousands of ballots were recorded toward Karzai's re-election.
The report cited unnamed senior Western and Afghan officials.
According to the latest figures from the Afghan election commission, Karzai now leads Abdullah Abdullah, his main challenger and former foreign minister, by 48.6 per cent to 31.7 per cent.
But the incumbent president is still short of the 50 per cent of the vote needed to avoid a run-off.
The final tally of votes is scheduled for this week, but authorities still have to investigate over 2,000 allegations of election fraud.
As internal tensions over the election mount, Nato allies Germany and the US are locked in what could become a major dispute over a German-ordered air raid by US fighters that appears to have killed Afghan civilians.
Afghan and Nato officials have already begun investigations into the attack in the northern province of Kunduz.
Afghan officials say up to 70 people were killed in the early morning air raid on Friday, which targeted two tanker trucks of fuel, hijacked by the Taliban, but around which villagers had gathered to syphon off petrol.
Both German and US officials have tried to deflect blame.
Franz Josef Jung, Germany's defence minister, said the Taliban's possession of the two tankers "posed an acute threat to our soldiers".
German officials have said the tankers might have been used as suicide bombs.
Angela Merkel, Germany's chancellor, has called for a "thorough and quick" Nato investigation into the incident.
Merkel and Gordon Brown, the British prime minister, have also called for an international conference on the future of Afghanistan to be held before the end of the year
"It should follow the work that is ongoing in all our countries to look at what is the best pathway forward for Afghanistan," Brown said in a joint press conference after talks with the German leader.