The 57-year-old lawyer from the nothern state of Haryana had defeated political heavyweight Sharad Pawar 16-15 in the BCCI election on September 29, thanks to outgoing president Jagmohan Dalmiya's casting vote.
The election was challenged by Pawar's supporters in India's Supreme Court, which ruled in favour of Mahendra earlier this month and ordered the BCCI to call a general body meeting to ratify his appointment.
Dalmiya, one of India's best-known sports administrators who once headed the International Cricket Council (ICC), had led the BCCI in the interim till Thursday's meeting.
However, an earlier decision to make Dalmiya the BCCI's first patron-in-chief and also India's representative on the ICC, which had also been challenged in a lower court in Madras, was put on hold pending the court's verdict.
"I don't know who will represent the board at ICC meetings, it all depends on what the court says," Dalmiya told reporters on Thursday.
Mahendra, son of former Haryana chief minister Bansi Lal and a self-confessed protege of Dalmiya, had earlier served as BCCI secretary in the 1980s and was one of its five vice-presidents till last year.
He did not attend Thursday's general body meeting due to political engagements in Haryana where he is contesting next month's legislative elections.
Mahendra's immediate task will be to organise next month's high-profile tour by Pakistan for three Tests and five one-day internationals.
It will be Pakistan's first tour of India since 1999 and follows India's visit in March-April, 2004 for their first Test series on Pakistan soil in 15 years.