Htin Kyaw, 69, hailed his elevation to the top post as "Suu Kyi's victory", a clear nod to her plan that he serve as a proxy for the Nobel laureate who is constitutionally barred from becoming president.
MPs erupted into applause after the result was announced following a lengthy ballot count by hand in the capital Naypyidaw, in which Htin Kyaw took 360 of 652 votes cast.
Suu Kyi's National League for Democracy won a thumping victory at elections in November, allowing her party to dominate Myanmar's two legislative houses.
But the military remains a powerful force and has refused to change a clause in the junta-era constitution which bars her from the presidency.
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The veteran activist has instead vowed to rule "above" the next leader. Her choice of Htin Kyaw is seen as a testament to her absolute faith in his loyalty.
The affable economics graduate, who acted as a driver for Suu Kyi in brief spells of freedom from her long years of house arrest, has the democracy movement in the family.
Htin Kyaw will be sworn in on March 30, replacing incumbent Thein Sein. It will be the first time Myanmar has had a civilian president since 1962, when the military seized power.
Thein Sein, a former general, led a quasi-civilian reformist government for the last five years that has been praised for moving the nation out of the shadow of outright military rule.
For many MPs from Suu Kyi's party Tuesday's vote was a vindication of their long years of struggle for democracy under the repressive former junta, which locked up hundreds of dissidents as it tried to stifle criticism.
Zin Mar Aung, an NLD MP who was involved in 1988 protests and is herself a former political prisoner, termed the vote "very historic".