Mr Murdoch is chief executive of Fox, which is attempting to seize control of the 61% of Sky it does not already own.
There was a larger vote, however, against Sky's remuneration report. The majority of the other resolutions passed with over 90% support.
However, this was an improvement on a year ago, when more than 50% opposed Mr Murdoch's reappointment.
UK's Competition and Markets Authority (CMA) has set out more details about what it intends to examine in its investigation into the proposed takeover of Sky Plc by 21st Century Fox, which owns STAR India.
Some institutional shareholders had criticized Murdoch's appointment as chairman, arguing that could pose a conflict of interest given his role as CEO of Sky's largest shareholder.
The pay package handed to Sky's chief executive, Jeremy Darroch, quadrupled to more than £16m in the year to the end of June, despite a hefty fall in annual profits at the broadcaster's United Kingdom and Ireland business.
One shareholder, who did not give his name, said to Murdoch: "I have the same problem with my dad".
In response to the question about the Fox News scandal, Darroch said the "whole board are incredibly supportive and behind Sky" and that it wanted to make a "broader contribution" to society.
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When asked by the culture, media and sport select committee about how the decision was reached White said that a thorough review had been carried out adding "We did not find a particular concern that would have caused us to believe that Sky News in particular and Sky as a broadcaster, post-transaction, would not be a fit and proper broadcaster", adding that Sky "currently has a very strong record of compliance on broadcasting".
The Sky AGM came as the company reported strong first quarter results, with 161,000 new customers and a 5 percent uptick in revenue of £3.3 billion.
Fox's US$15 billion bid for Sky is now with United Kingdom competition watchdogs.
Sky said it added 160,000 new customers in its first quarter, which marks a 51% rise on a year earlier.
He pointed out that in addition to Sky's existing markets - the UK, Ireland, Germany, Austria and Italy - the company had just launched consumer streaming services in Spain and Switzerland.
In terms of programming, Sky said Riviera became its most-watched original series ever in period, and Game of Thrones the most-watched series ever on Sky.
Shares of Sky, which are valued at 1075p under 21st Century Fox's takeover bid, were up 18p at 931.5p this afternoon.