Governor Bhagat Singh Koshyari administered oath to the saffron-clad Thackeray and six ministers at the sprawling Shivaji Park here, venue of the Sena's Dussehra rallies.
Those present at the ceremony included NCP chief Sharad Pawar, Madhya Pradesh Chief Minister Kamal Nath, senior Congress leaders Ahmed Patel and Mallikarjun Kharge, MNS chief Raj Thackeray and DMK leader MK Stalin.
Congress chief Sonia Gandhi was among those invited but she wasn't present. She sent congratulatory messages to Uddhav and MPCC chief Balasaheb Thorat, who was among the six ministers sworn in.
"Shiv Sena, NCP and the Congress have come together under quite extraordinary circumstances at a time when the country faces unprecedented threats from the BJP," Gandhi's letter said.
In a letter to Thorat, Gandhi expressed confidence that the Congress-NCP-Shiv Sena combine will provide a stable and responsive government.
Prime Minister Narendra Modi congratulated Uddhav Thackeray on taking oath as the CM of Maharashtra. "I am confident he will work diligently for the bright future of Maharashtra," Modi tweeted.
Thackeray took oath as chief minister over a month after results of the October 21 Maharashtra Assembly elections were declared on October 24.
Eknath Shinde, Subhash Desai (both Shiv Sena), Jayant Patil, Chhagan Bhujbal (both NCP), Balasaheb Thorat and Nitin Raut (both Congress) were sworn in as ministers.
Former Maharashtra deputy chief minister Ajit Pawar, his cousin and MP Supriya Sule, Uddhav's wife Rashmi, his MLA-son Aaditya, industrialist Mukesh Ambani, his wife Nita and son Anant were also present at the ceremony.
The Shiv Sena, NCP and Congress formed the government after the Thackeray-led party fell out with pre-poll ally BJP over sharing the chief ministerial post.
The BJP emerged as the single largest party winning 105 seats. The Shiv Sena, NCP and Congress won 56, 54 and 44 seats respectively in the 288-member Maharashtra Assembly.
Thursday's swearing in ceremony came after days of dramatic political developments, which included a three-day government formed by BJP's Devendra Fadnavis with unexpected support from NCP leader Ajit Pawar, who has since returned to the Sharad Pawar-led party fold.
There was speculation that Ajit Pawar would be sworn in as deputy chief minister on Thursday but only two ministers from the NCP took oath at the ceremony.
A special session of the 14th state Assembly was held here on Wednesday where oath was administered to 285 newly- elected members by pro tem Speaker Kalidas Kolambkar who was appointed to the post by Governor Bhagat Singh Koshyari.
Uddhav Thackeray is the 18th CM of Maharashtra.
However, considering the number of terms, he will be the 29th chief minister of the state.
An ace photographer, the otherwise affable, mild- mannered politician, displayed combative traits of his father in dealing with the BJP on the demand for rotational chief ministership just after Assembly poll results were announced.
In rallies, Uddhav had repeatedly voiced his resolve to fulfil the dream of his father to make a Shiv Sainik the chief minister, and ended up donning the mantle himself.
Hours before the swearing in ceremony, the Shiv Sena- NCP-Congress alliance said the Maharashtra Vikas Aghadi (MVA) government in the state would waive farmers' loans and ensure 80 per cent quota in jobs to the local youth.
NCP leaders Jayant Patil and Nawab Malik and Sena leader Eknath Shinde announced details of the Common Minimum Programme (CMP) of the alliance.
Sena's most discussed promise during the Assembly poll campaign -- a full meal at Rs 10 -- also figures in the CMP.
A law will be enacted to ensure 80 per cent job quota for locals/domicile youth, it said.