It dropped sitting MP from Guna, Krishnapal Singh Yadav, to field Union Minister Jyotiraditya Scindia from the seat.
Thackeray was speaking virtually after the inauguration of a water taxi service, linking Navi Mumbai to south Mumbai, and the Belapur jetty in the neighbouring township.
Flash floods triggered by torrential rain have killed at least 22 people in India and forced more than 1,70,000 from their homes.
Sounding the Congress' poll bugle in the state, Gandhi attacked the Modi government repeatedly alleging that it was working with an approach of 'Hum do, Hamare do' -- a term he recently used while speaking in Lok Sabha to claim that the country is being run by only four people.
Governor Acharya Devvrat administered the oath of office and secrecy to the 52-year-old Thakur, a five-time MLA from Seraj, and other ministers which included six new faces.
Assam Chief Minister Sarbanand Sonowal condemned the fatwa and directed police to provide security to the singer.
'We want to protect our history, we want to protect our people from getting overwhelmed by the influx from Bangladesh, that is why the people of Assam are out in the streets,' says former Assam chief minister and Asom Gana Parishad leader Prafulla Kumar Mahanta.