BJP’s Y Khemchand was earlier elected the Speaker.
The floor test took place 11 days after assembly elections threw up a fractured verdict and five days after the Biren Singh ministry was sworn in.
In the 60-member house, the BJP won 21 seats and the Congress 28.
But the BJP joined hands with the Naga People’s Front (NPF) and National People’s Party (NPP), which have four legislators each, as well as an independent and a member each from the LJP and Trinamool Congress.
Also, Congress MLA T Shyamkumar defected to become a cabinet minister.
Speaker Khemchand too was elected by voice vote, defeating Govindas Konthujam of the Congress.
Congress leader and former Chief Minister Okram Ibobi Singh conceded defeat but insisted that his party should have been called first to form the government as it was the single large group in the house.
BJP sources said the portfolios would be allocated to the ministers soon.
The Manipur Chief Minister is allowed to have 12 ministers. He already has nine.
(With IANS inputs)