The hung verdict will reset the political calculations as no party is in the position to rule the country's richest civic body on its own and alliance seems inevitable.
However, it is not yet clear whether the saffron allies, who share power both in Maharashtra and at the Centre, will get back together or new combinations will emerge.
AIMIM, which had made its maiden entry into the Maharashtra Assembly with two seats in the last polls, won three seats on debut in the BMC elections, Samajwadi Party six, Akhil Bhartiya Sena one and Independents four.
The results came as a shot in the arm for Chief Minister Devendra Fadnavis, who spearheaded the BJP's campaign with focus on transparency. The BJP also came out with flying colours in other municipal corporations and local bodies.
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The BJP's victory came as a major morale-booster for the party which is in the midst of gruelling assembly polls in five states, including key battleground state of Uttar Pradesh, where it is pitted against strong opponents.
The calumny-filled campaign for control of BMC had even cast a shadow on the stability of the state government, with the Sena threatening to walk out and putting the government on notice.
In the outgoing civic body, Sena had 89 seats, BJP 32, Congress 51, NCP 14, SP 8, MNS 28, PWP 1, and Independents 4.
Thanking the voters, an elated Fadnavis said, "Our victory is the result of people's acceptance of our agenda of transparency," and indicated that his party's core committee would explore the options before it.
Meanwhile, when asked about the future course of action, Sena leader Uddhav Thackeray said, "What is the hurry? Wait for some time. We have not yet decided if an alliance has to be made or not. We will do so soon."
With the Congress getting reduced to 31 seats, its city
unit president Sanjay Nirupam, who had crossed swords with senior leader Gurdas Kamat ahead of the polls, offered to quit, owning responsibility for the rout.
The voters dealt a heavy blow to Raj Thackeray's MNS whose tally fell to mere 7 from 28 in 2012, primarily due to a huge consolidation of Marathi votes in favour of Shiv Sena.
As the BJP put up a sterling performance in civic polls across state including the BMC, Fadnavis said the victory was a vote for transparency and demonetisation.
As no party is in the position to rule the BMC on its own and the saffron allies are looking in opposite directions, it now remains to be seen how the major players cobble together an alliance which has enough numbers to control the civic body.
When asked about this, Fadnavis said the party's core committee will decide the future course of action.
Since the last two days, the BJP has been trying to send the signal that it did not want the bitterness of the campaign to continue.
In his interview to a newspaper, Fadnavis recently said the post-poll alliance will be on "transparency" alone.
State BJP president Raosaheb Danve told reporters, "Everybody needs to forgive and forget the allegations as well as the strong language used during the campaign. Now, the mandate is out and we respect it."
Thackeray, on his part, asserted that the city Mayor would be from the Sena, an indication that he could go for a hard bargain if the two saffron parties were to come together again.