Obama called the Nobel Peace Prize winner who spent more than a decade under house arrest and praised her "tireless efforts and sacrifice over so many years to promote a more inclusive, peaceful and democratic Burma."
Obama also spoke to Myanmar President Thein Sein to hail an election that many hope could offer the country a peaceful way out of decades of suffocating military rule.
"The two leaders discussed the importance for all parties to respect the official results once announced and to work together with a spirit of unity to form an inclusive, representative government that reflects the will of the people" the White House said.
The White House has been keen to stress that the vote is an important step on a much longer path toward democracy.
It said Obama told both leaders "that the election and formation of a new government could be an important step forward in Burma's democratic transition and the effort to forge a more peaceful and prosperous future."
Obama put his own political standing on the line by traveling to Myanmar last year to urge the country's rulers to loosen their iron grip on power and embrace change.
White House officials have suggested that further sanctions relief and assistance could be in the pipeline.
But with Suu Kyi barred from becoming president under the current constitution and a plethora of problems with the treatment of Myanmar's ethnic and religious groups, Washington may be cautious to move quickly.
Suu Kyi has vowed to rule from "above the president," indicating she will use a proxy to sidestep the bar on her taking the top office.
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