The 52-year-old politician won almost 80% of vote in Central Asian nation, preliminary results cited by Central Election Commission showed, meaning there will be no run-off.
Violent protests in the volatile Asian country erupted after a disputed parliamentary election.
Embattled Kyrgyz President Sooronbay Jeenbekov has declared a state of emergency in the capital Bishkek, under which soldiers have orders to prevent armed clashes.
Clashes between vigilantes and protesters trying to force their way into government buildings mark a growing sense of unease in a country that suffered violent revolts in 2005 and 2010.
Ahead of the announcement, opposition supporters in Kyrgyzstan had seized several government buildings in the country's capital, freed ex-president Atambayev from jail and announced plans to oust the president and form a new government.
Two establishment parties look set to dominate parliament, but it remains unclear if they can form a grand coalition after a series of internal rifts plagued the previous ruling alliance.
The country's head of security forces accused Almazbek Atambayev of planning a coup before he was detained in raids on his compound last week, state news agency Kabar says.
Kyrgyz forces were reported pulling out of a village after an unsuccessful raid to try to arrest the country's ex-president Almazbek Atambayev at his residence in an operation that left one serviceman dead and dozens of people injured.
Initial results placed former Kyrgyz premier Sooronbai Jeenbekov ahead in the presidential poll at 55 percent, while his main opponent oil tycoon Omurbek Babanov lagged behind at 34 percent.
The journey from uprisings in 2005 and 2010 to a vote that could secure an unprecedented peaceful transfer of power between two elected presidents has not been easy for the landlocked nation of six million.
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