"As we all know, 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," Mr. Obama said in the Oval Office after a meeting with Iraqi Prime Minister Nouri al-Maliki. "We are pleased with the steps that have been taken today, and we hope that we can build on this progress."
This morning, current Afghan President Hamid Karzai said he accepted the findings of the country's election commission --which found that he received less than 50 percent in the first round voting in August. That set up a November 7 runoff between Karzai and former Foreign Minister Abdullah Abdullah.
CBSNews.com Special Report: Afghanistan
Mr. Obama said he spoke with Karzai this morning, congratulating him on accepting the result.
"President Karzai, as well as the other candidates, I think, have shown that 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.
During his remarks, Mr. Obama also thanked troops stationed in Afghanistan as well as U.S. Ambassador Karl Eikenberry and Sen. John Kerry, D-Mass., who stood alongside Karzai during his news conference this morning.
In a written statement released earlier in the morning, Mr. Obama called the runoff an "important step forward" and called on "all elements of Afghan society continue to come together to advance democracy, peace and justice."
Other members of the administration have also weighed in on the developments in Afghanistan as well. Secretary of State Hillary Clinton said in a statement she welcomed the announcement, saying that "Afghans showed today that their processes work." She also pledged U.S. support for the second round of voting.
"Afghanistan has been through a rough and contentious election. The bravery, patience, and resilience of the Afghan people has been on display since election day, when so many of them went to the polls in the face of threats and intimidation," the statement read. "We pledge our support to the election authorities to help them achieve a conclusion to the elections process. We remain committed to partnering with the Afghan people and their government on our shared objectives of strengthening good governance, tackling corruption, increasing economic opportunities and improving security for all Afghans."
The announcement this morning also raised questions about the administration's deliberations over strategy and troop levels in the country. But Secretary of Defense Robert Gates warned during a trip to Asia that the U.S. cannot "sit on our hands" waiting on the election results, the Associated Press reports.
White House Press Secretary Robert Gibbs maintained the same posture on when a decision would be made, saying that it would be "in the coming weeks." Gibbs also said that the next meeting of the president's so-called war council would be next early next week.
Also of note is that Gibbs tried to make clear this morning that the election is to be decided by the Afghan people and that the administration does not have a preference for a winner.
"The U.S. doesn't have a candidate in this election," Gibbs told reporters.
Mr. Obama also mentioned Abdullah, Karzai's opponent, in the written statement.
"I congratulate President Karzai and Dr. Abdullah, who both earned the support of voters from across the country," Mr. Obama added. "I also commend all of the other presidential candidates who made this such a vibrant campaign."
Update 4:28 p.m. ET: The White House announced that Mr. Obama also called Abdullah today "to express appreciation for his constructive efforts."
Karzai to Face November Afghan Runoff Vote
Gates: U.S. Can't Wait on Afghan Election
CBS Evening News Reports: The Road Ahead