The upper house voted for the impeachment last month.
The impeachment was supported by all political parties, including the ruling Union Solidarity and Development Party (USDP) — which has close ties to the military — as well as Aung San Suu Kyi’s National League for Democracy.
In a speech to parliament before the vote, USDP lawmaker Soe Yin said there was a need for “checks and balances” within the new political system.
Only the unelected military representatives who occupy one quarter of the seats in the legislature opposed the impeachment.
The row erupted after the court, in response to a request by President Thein Sein to study the issue, issued an order in February which limited the power of parliamentary committees and commissions to summon ministers for questioning.
It was seen as the country’s first major political crisis since decades of military rule ended last year, pitting the government against the parliament — and in particular lower house speaker Shwe Mann, a top regime figure and former general considered a possible contender to replace Thein Sein when he retires.