He has been relieved by the Supreme Court of his responsibilities at Board of Control for Cricket in India (BCCI) with immediate effect, NSE said in a statement.
Limaye was appointed to a panel, set up by Supreme Court, to administer the BCCI.
"He will be joining the NSE as Managing Director and CEO from Monday, July 17, 2017," the exchange said.
Last month, markets regulator Sebi cleared Limaye's appointment as head of NSE, provided he gives up his role at BCCI.
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Limaye, who joined IDFC in 2005, has over 25 years of experience with financial institutions, global investment banks, international commercial banks and global accounting firms.
He started his professional career with Arthur Andersen in Mumbai in 1987 and has also worked with Ernst & Young and Citibank. He has worked at Wall Street for eight years, with Credit Suisse First Boston before returning to Mumbai in 2004.
A commerce graduate, Limaye is an MBA in Finance and Multinational Management from the Wharton School of the University of Pennsylvania.