Calling the development a "black day" in the history of the state, the two opposition parties announced that they would register their protest with Governor C Vidyasagar Rao.
Earlier, BJP MLA Ashish Shelar moved a one-line motion seeking confidence of the House in the Devendra Fadnavis-led government, which was put to a voice vote by Speaker Haribhau Bagde.
As the legislators supporting the motion exclaimed "Aye", the Speaker declared it passed, triggering a storm of protest among Shiv Sena and Congress MLAs, who rushed to the Well of the House. Sena earlier in the day formally decided to occupy the main Opposition's space in the Assembly.
During the proceedings, members of NCP, which had offered outside support to the BJP government, remained quietly seated.
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Sena had earlier staked its claim to the Leader of Opposition's position and the Speaker had said he would take up its demand after the trust vote as Congress too had demanded the post on the grounds that Sena continues to be a constituent of the BJP-led NDA.
Led by Shinde, Sena MLAs again took up their protest and called for the confidence motion to be determined by a division of votes.
BJP has 121 MLAs and, together with NCP's 41, has the support of 162 MLAs, 18 more than required for a majority in the House which has an effective strength of 287. The party has also claimed the support of seven Independents, three of Bahujan Vikas Aaghadi and some others from smaller parties.