The proposals to re-appoint J J Irani and Keki Mistry as directors on the HDFC board were also approved by the shareholders.
According to reports, some US proxy advisories had asked investors to vote against Parekh over his directorship and independence of company's board.
The voting results are surprising, Indian proxy advisory firm IiAS Founder Amit Tandon said.
It could be on the advice of some proxy advisory firm but it is not clear what was the real reason for the opposition to Parekh's re-appointment, he noted.
As per the Companies Act, votes cast in favour of a special resolution should be not less than three times the number of the votes, if any, cast against the resolution.
HDFC had to come out with special resolution for re-appointment of Parekh as he would cross the age of 75 years in October 2019.
The mortgage lender had sought approval for continuation of directorship of J J Irani who has attained the age of 75 years, up to the expiry of his present term as an Independent Director (July 20,2019).
As many as 94.58 per cent of the shareholders voted in favour of Irani.
Keki Mistry's re-appointment as Managing Director -- designated as Vice Chairman and Chief Executive Officer -- for a period of three years.
Mistry got 99.51 per cent votes of shareholders and his re-appointment was through an ordinary resolution.
Upendra Kumar Sinha and Jalaj Ashwin Dani were appointed as Independent Directors at the annual general meeting.
In the latest June quarter, HDFC reported a 54 per cent increase in standalone net profit at Rs 2,190 crore, mainly due to Rs 511 crore dividend it received from HDFC Bank.
Shares of HDFC closed at Rs 1,994.75, down 1.64 per cent on the BSE today.