Obama, in a telephonic call, congratulated Karzai for agreeing to the run off on November 7 with his rival and former foreign minister Abdullah Abdullah on the direction of Afghan's Independent Electoral Commission.
"I had the opportunity to speak with President Karzai this morning, and I wanted to congratulate him on accepting the certification of the recent election," Obama said at a joint press conference along with Iraqi Prime Minister Nouri Al-Maliki, at the White House.
"...this has been a very difficult time in Afghanistan to not only carry out an election under difficult circumstances, where there were a whole host of security issues that had to be resolved, but also post-election a lot of uncertainty," he said.
"President Karzai, as well as the other candidates have shown they have the interests of the Afghan people at heart, that this is a reflection of a commitment to rule of law and an insistence that the Afghan people's will should be done. And so I expressed the American people's appreciation for this step," he said.
The commission decided to announce a reelection after finding that Karzai had won only 49.7 per cent of the August 20 vote which is still below the 50 per cent threshold needed to avoid a runoff.
Acknowledging that there are violent forces opposed to democracy in Afghanistan, Obama said elections took place despite such adverse conditions. "Despite these very difficult conditions, what we've seen is elections take place, we have now seen the IEC and the ECC in Afghanistan complete their work, we have seen candidates expressing a willingness to abide by constitutional law, and there is a path forward in order to complete this election process," he said.
Obama said his administration will continue to work with international organisations as well as the Afghan government, to ensure that Afghanistan moves towards peace and security and prosperity, and that the will of Afghan people is ultimately done.
Earlier, US Secretary of State Hillary Clinton in a statement termed the decision of Karzai as in the best interest of Afghanistan. "I welcome President Karzai's announcement that he accepts the recommendations of the commission's statement on the August 20 first round election results," she said.
"The leadership shown by the President (Karzai), his rival Abdullah and all other candidates has strengthened Afghanistan and kept faith with the best interests of the Afghan people," Clinton said in a statement. Welcoming the decision, Senator John Kerry, Chairman of the Senate Foreign Relations Committee, who is currently in Afghanistan, termed Karzai as a statesman.
"Today, President Karzai showed statesmanship by deciding to move forward, and to strengthen the country by embracing the constitution and the rule of law," Kerry said in Kabul.