Htin Kyaw, 69, hailed his elevation to the top post as "Suu Kyi's victory", a clear nod to her plan for him to serve as a proxy for the Nobel laureate who is constitutionally barred from becoming president.
MPs erupted into applause after victory was announced following a lengthy ballot count by hand in the capital Naypyidaw in which Htin Kyaw took 360 of 652 votes cast.
Myanmar is in the grip of a stunning transformation from an isolated and repressed pariah state to a rapidly opening aspiring democracy.
But the military remains a powerful force in the Southeast Asian nation and has refused to change a clause in the junta-era constitution that bars Suu Kyi from top political office.
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The veteran activist has instead vowed to rule "above" the next leader.
Her choice of Htin Kyaw to act in her place is seen as a testament to her absolute faith in his loyalty.
"This is sister Aung San Suu Kyi's victory," the newly elected president told reporters after the vote. "Thank you."
The two other candidates who were also running in Tuesday's election will now become the country's joint vice presidents.
They are retired general Myint Swe, an army-backed candidate who remains on Washington's sanctions list and won 213 votes, and ethnic Chin MP Henry Van Thio, who gathered 79 votes.
Most of Myint Swe's votes came from the army's parliamentary bloc, which is reserved a quarter of seats in parliament, and from military-backed parties.
Her party's huge election victory was seen as a further endorsement of her political star power, as millions were swept to polling stations by the NLD's simple message of change.
But the military still retains significant power, including control of the vital home, defence and border ministries.
Months of negotiations with army chief Min Aung Hlaing failed to remove the obstacles blocking Suu Kyi from power.