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Shelly Oberoi received 150 votes while Rekha Gupta 116 out of the total 266 polled in the election held after a decisive victory for AAP in the Supreme Court.
Delhi Chief Minister Arvind Kejriwal and Deputy Chief Minister Manish Sisodia congratulated Ms Oberoi and the party workers. "The goons have lost, the public won. Today in the Municipal Corporation of Delhi, the people of Delhi won and hooliganism was defeated," Mr Kejriwal said.
Since the civic elections in December, which the AAP won, the mayoral elections were postponed thrice amid a prolonged tussle between the AAP and the BJP.
Ms Oberoi had approached the top court, challenging the BJP's contention that the aldermen - 10 members nominated by the capital's Lieutenant Governor, a representative of the BJP-led government at the centre - are allowed to vote in the election.
Judges led by Chief Justice of India DY Chandrachud said nominated members cannot vote in the election. "Nominated members cannot go for election. The constitutional provision is very clear," the court observed.
After the election of the mayor, AAP's Aaley Mohammad Iqbal was elected Deputy Mayor. Next, six members of the Standing Committee will be elected. In the election for the Standing Committee, AAP is likely to win three seats and the BJP two. The fight is over the sixth seat.
If the alderman were allowed to vote, the strength of the BJP would have gone up to 123 from 113. AAP has 150 votes in the 274-member house, where the majority mark stands at 138.
So, while it would not have affected the outcome of the mayoral election, the BJP could have scooped up a critical chunk of the Standing Committee, understood to be the most powerful body in the civic body. The Congress has said it would abstain, sparking allegations of "deal-making with the BJP" from AAP councillors.
AAP won 134 of 250 wards in the first municipal election held after the merging of the MCD and redrawing of constituencies last year. The BJP finished second after controlling the civic body for 15 years.
AAP had earlier objected to Lieutenant Governor VK Saxena naming the 10 aldermen without consulting the Delhi government. Oath-taking by the 10 nominated aldermen and the question of their voting had stalled the mayor election thrice. The election was postponed the fourth time to accommodate the Supreme Court hearing.
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