The Southeast Asian nation, choked for decades under junta rule, is on the cusp of a remarkable political transition after Suu Kyi's National League for Democracy (NLD) thundered to victory in November elections.
Myanmar's people are hoping her government can reboot a country eviscerated by half a century of army rule that battered the economy and repressed dissent.
"Even though there were difficulties and challenges, we were able to bring a democratic transformation eventually," Thein Sein said addressing the military-stacked legislature for the last time.
"This is a triumph for all Myanmar's people," he added.
"As everyone knows, for over five decades we were far away from a multi-party democratic system," he said.
Thein Sein, who under drawn-out handover rules retains his post until the end of March, has been a key player in Myanmar's astonishing reform process so far.
He was among a host of military figures who shed their uniforms to form a government in 2011.
Initially that government was viewed with suspicion as a civilian front for the army's continued domination of the country from behind the scenes.
While the army retains major clout, sweeping political and economic reforms since 2011 have surprised the international community, encouraging a flood of foreign investment.
They culminated in November's polls which passed peacefully and fairly and saw Suu Kyi's party scoop nearly 80 per cent of elected seats in the national parliament.
Thein Sein's party was all but annihilated in the legislature.
Both he and powerful army chief Min Aung Hlaing have pledged to support the transition towards democracy in the face of Suu Kyi's popular mandate.
The new NLD MPs, many of whom are political novices from a diverse range of professions, will take their seats on February 1 following the final day of a lame duck session by the out-going parliament on Friday.
A flurry of political plays have dominated the days leading up to the handover, leaving analysts struggling to decipher their meaning in a country where decision-making has long been made in secret.
Suu Kyi met Min Aung Hlaing on Monday and a day later a proposal emerged to extend the remit of the powerful home affairs ministry, which is controlled by the military.
The 70-year-old Suu Kyi is currently barred from becoming president by the junta-era constitution that many believe was designed specifically to exclude her.
She has vowed to rule through a proxy, who is yet to be named in public.
Observers say the former political prisoner is seeking to find ways to placate a twitchy military, which maintains huge political and economic sway.
- AFP