Deshmukh is a veteran leader of Congress, NCP's ally in the previous government with which it fell out ahead of the Assembly elections last year.
As many as 45 members voted in favour of the motion and 22 against it. The motion had been moved by NCP, the largest party in the upper house, last week.
Those who voted in favour included 27 members of NCP and 12 of BJP. Shiv Sena, BJP's partner in the ruling coalition, abstained from voting, before calling the motion a murder of democracy.
NCP group leader Sunil Tatkare said in the house that his party was not casting aspersions on Deshmukh's integrity.
"You don't have the requisite number in the Council, still you refuse to part with the post, does it not show your hunger for power? We are not at all against his personal stature. We all respect him highly. It is the malicious ideas that are being planted in his head by the Congress that we are against," Tatkare said.