However, Thackeray parried a query on whether the BJP-led state government was still on a "notice period".
"Our fight against 'Bhampakpana' (hyporcitical agenda) would continue," Thackeray said.
In run-up to the bitterly-fought civic polls, including Mumbai, Thackeray had last month said the Fadnavis government was on a notice period, fuelling speculations about its stability as the Sena is an important alliance partner in the NDA dispensation.
On the BJP corporators voting in favour of Sena nominee Vishwanath Mahadeshwar in the BMC general body meeting, who was elected Mayor, the Sena chief said it was really "pleasing".
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"We got full mandate in Thane, but fell marginally short in Mumbai (civic polls). But it's good to have got their (the BJP's) support in Mumbai," he said.
Thackeray also thanked the BJP government for the progress it had made in implementing the Bal Thackeray memorial project.
Yesterday, the state Legislative Assembly had cleared a bill paving the way for construction of the memorial in Mayor's bungalow in Shivaji Park in Central Mumbai.
Mahadeshwar and Hemangi Worlikar, both nominees of Sena for the posts of Mayor and deputy-Mayor, respectively, got a walkover as the BJP had withdrawn from the Mayoral race in a tactical move.
In a hung verdict in the 227-member BMC, Sena had won 84 seats while the BJP 82. The next largest bloc in the civic body was Congress (31).
Thackeray, however, evaded queries on the formation of alliances in Zilla Parishads, which went to polls last month, where the BJP has done well.
The Sena chief had a dig at the BJP corporators who took a oath of transparency in the civic body today.
(Reopens BES 22)
Taking at a dig at the BJP corporators for shouting slogans hailing Prime Minister Narendra Modi even as the new Mayor was being elected, he said it would have been better had they raised Chhatrapati Shivaji's name.
In a veiled reference to the BJP, Thackeray said he was thankful to all the known and the unknown persons who supported the Sena while the new Mayor was being elected.
"We will not forget the martyrs who gave up their lives only for a united Maharashtra. We will continue to struggle against wrongdoings," he said.