Htin Kyaw, a respected writer and longtime close friend of Suu Kyi, is virtually guaranteed to sweep the board, with both legislative houses dominated by the Nobel laureate's National League for Democracy thanks to its election landslide in November.
"We are going to start electing the president now," parliament speaker, Mann Win Khaing Than told lawmakers. Suu Kyi was the first to cast her vote.
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.
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.
"We have planned to vote for Htin Kyaw and practised not to make any mistake," said an NLD MP who asked not to be named after attending an instruction session by the party on Monday afternoon.
Myanmar's new president will replace incumbent Thein Sein at the end of the month following five years of army-backed quasi-civilian leadership that has been lauded for steering the nation out from the shadow of outright military rule.
Tuesday's vote will see 652 legislators chose from three candidates, one put forward by each of the two legislative chambers and a third proposed by the military, who are reserved a quarter of seats in parliament.
The two other candidates are ethnic Chin MP Henry Van Thio, a Suu Kyi ally put forward by the upper house, and the military's nominee Myint Swe, a retired army general still blacklisted by the United States.
Suu Kyi, 70, has unrivalled popularity both as the daughter of the country's independence hero and as a central figure in the decades-long democracy struggle.
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.
Months of negotiations with army chief Min Aung Hlaing have failed to remove the obstacles blocking her from power.
Suu Kyi is barred from the presidency by a clause in the charter because she married and had children with a foreigner.
It is not yet clear what role she plans to take or how she will manage the relationship with the country's new president.
A new cabinet, set to be announced at the end of the month, is expected to include figures from across the political spectrum as Suu Kyi looks to promote national reconciliation.
It will swiftly set about facing the country's many challenges, including poverty, civil wars in ethnic minority borderlands and decrepit infrastructure.
Senior party figures say one of the government's first tasks will be to whittle down myriad ministries by combining overlapping portfolios.
While little known outside Myanmar, Htin Kyaw, who helps run her charitable foundation, commands considerable respect inside the country, partly because his father was a legendary writer and early member of the NLD.
He is married to sitting NLD MP Su Su Lwin, whose late father was the party's respected spokesman.
The military's choice of Myint Swe, seen as a hardliner and close ally of former junta leader Than Shwe, however is proving controversial in a nation still smarting from half a century of army dominance.//AFP