Suu Kyi's opposition National League for Democracy (NLD) has won more than 80 percent of the seats declared so far in the lower house, a result that puts her on course to form the new cabinet, and is well ahead in the upper house and regional assemblies.
If the full results confirm the trend, Suu Kyi's triumph will sweep out an old guard of former generals that has run Myanmar since Thein Sein in ushered in sweeping democratic and economic reforms four years ago.
"US President Obama congratulated the President and the entire government on having been able to hold a historic free and fair general election," said presidential spokesman and Information Minister Ye Htut on his Facebook page.
"He said America would continue cooperating with the Myanmar government." Obama has visited Myanmar twice in the past three years, hoping to make its transition to democracy a foreign policy legacy of his presidency.
Thein Sein and the powerful army chief Min Aung Hlaing have already endorsed Suu Kyi's victory, congratulating her on Wednesday on winning the majority of the seats in the first free election in 25 years.
The two reiterated their commitment to respect the result and agreed to Suu Kyi's request to hold reconciliation talks soon, although the parties are still to agree on the details. Such unambiguous endorsements of Suu Kyi's victory could smooth the lengthy post-election transition, ahead of the first session of parliament which reconvenes on Monday.
It also sets the stage for cooperation between democratic activists and the army, which had fought them during half a century of iron-fisted rule before a handover to a semi-civilian government in 2011.

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