Masses of Afghan voters lined up outside polling stations -- with a final turnout election officials say could exceed 50 percent -- to pick a successor to President Hamid Karzai for the first time since the US-led invasion in 2001.
Karzai has refused to sign a security agreement that would allow the US to keep around 10,000 troops in Afghanistan to train local forces and hunt Al-Qaeda, and relations with Washington have dropped to a new low.
Obama, in a statement, congratulated the Afghan voters "on behalf of the American people."
The elections "promise to usher in the first democratic transfer of power in Afghanistan's history" and "represent another important milestone in Afghans taking full responsibility for their country," he said.
"These elections are critical to securing Afghanistan's democratic future, as well as continued international support."
The US president urged election officials to make their formal decision on the outcome fairly, "knowing that the most critical voices on the outcome are those of Afghans themselves."
"The United States continues to support a sovereign, stable, unified and democratic Afghanistan," he added.
Obama also paid tribute to the Americans who have lost their lives or otherwise made sacrifices in and for Afghanistan.
Since the United States toppled the Taliban regime in 2001, 2,316 American troops have been killed, according to iCasualties.Org, which uses Pentagon data to estimate combat losses.
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