U Win Myint, a former barrister and speaker of the country’s lower house, won overwhelmingly with 403 out of 636 votes.
The 66-year-old beat the military candidate and acting president Y Myint Swe by nearly 200 votes in a country which just three years ago ended 50 years of total military control.
Myanmar’s military legacy still continues amid a slow transition to democracy, with the generals still in charge of security and guaranteed a quarter of parliamentary seats.
Nobel Peace Prize winner Ms Suu Kyi has retained her executive authority over the government, meaning she is “above the president”, she explained in 2016.
The de facto leader is not allowed to lead the country as the constitution, drawn up by the military in 2008, bans anyone with a foreign spouse or child from becoming president.
It targeted Ms Suu Kyi, who spent nearly 15 years under house arrest fighting for democracy, as her late husband was British, as are her two sons.
Ms Suu Kyi’s civilian government, under her National League for Democracy party, has struggled to implement peace and national reconciliation as the military continues to fight against ethnic rebels.
She has come under heavy global criticism for not speaking up about the plight of the Muslim Rohingya minority in oil-rich Rakhine state.
However, in the country she is still widely regarded as a heroine, with supporters saying her hands are tied by the military.
But there is hope Mr Win Myint will help lead the country out of the control of the generals, who are steadily ageing and not being replaced when they die.
The new president fought alongside Ms Suu Kyi during the 1988 democracy movement which was violently quashed by the military junta.
He was taken political prisoner with Ms Suu Kyi for the up-rising and was jailed several times since during the country’s military rule.
He reportedly missed being by his son’s deathbed after military intelligence said he could only see his son if he gave up politics.
The former geologist and lawyer has been known to reprimand military-linked MPs in parliament, especially those who have not prepared enough for debates.
His win has been welcomed by fellow MPs who are looking to him to follow through on protecting farmers’ rights, a crucial topic in the country.
Myanmar was forced to hold an election after outgoing president, Hytin Kyaw, also a close ally of Ms Suu Kyi, retired “in order to take rest from the current duties and responsibilities” amid speculation over his health.
Mr Win Myint is expected to be sworn in on Thursday.