He defeated his lone rival Elangbam Dijwamani of the opposition Congress by a margin of 18 votes.
In the 60 member Manipur assembly, Bhabananda secured 39 votes while Dijwamani got 21 votes.
The BJP and its allies have 38 members.
Chief Minister N. Biren Singh has been saying that more Congress MLAs are joining his party.
Six of them had already joined the BJP, whittling away the strength of the Congress which secured 28 seats to 22.