Formalities of his election were completed in the special sitting to enable him conduct business of the Upper House during the Monsoon Session of the legislature beginning July 18.
The newly elected members of the Council also took oath.
Nimbalkar's election to the post of the presiding officer was a mere formality as he has the support of Congress too.
The NCP leader was re-elected to the Upper House unopposed last month.
Nimbalkar was administered oath of office by Pro-tem Chairman Jayant Patil of Peasants and Workers Party.
The post fell vacant after the incumbent Vasant Davkare of NCP lost the Council election from the Thane local bodies constituency to Shiv Sena's Ravindra Phatak last month.
Congress has claimed its right on the Deputy Chairman's post.
(Reopens BES7)
Shivsangram leader and president of Shivaji Memorial Project Committee, Vinayak Mete, who was to take oath, was not present in the House.
Mete, whose organisation is an alliance partner of BJP, was elected to the Council last month from the BJP quota.
There was speculation that Mete, who holds minister-level rank as chairman of the committee, skipped oath-taking as he was unhappy over not being inducted in the Fadnavis ministry.