The Indian rupee fell 1.2% against the US dollar and stocks were also lower as investors reacted to his departure.
On Monday, Urjit Patel resigned from his post midway through his three-year term, citing "personal reasons".
His exit comes amid reports of a rift between the Reserve Bank of India (RBI) and the government.
Analysts expected Mr Patel's resignation could make investors more wary of India and hurt the economy as it prepares for a general election next year.
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