Martin Gilbert, the deputy chair, said the board had looked at the Fox takeover in the best interests of shareholders and had impartial discussions that did not include Murdoch or other Sky directors with connections to Fox.
During the meeting, one investor questioned both the terms of the deal and Mr Murdoch's position as chairman of Sky, given his role as 21st Century Fox's chief executive.
Almost half of independent shareholders voted to oppose Mr Murdoch's reappointment amid concerns over his role as chief executive of 21st Century Fox, which is attempting to seize control of the 61% of Sky it does not already own in an £11.7 billion deal.
Almost 22% of all shareholders, and more than 48% of independent ones, opposed Murdoch being allowed to continue in the post.
A Sky spokeswoman said Mr Murdoch was "uniquely well-placed" to be chairman.
In a stock exchange announcement detailing the AGM vote, Sky said: "The board is pleased that the majority of resolutions have been passed with a high level of support from shareholders".
(FOX), which has agreed to take full control of Sky, in a deal now being scrutinized by United Kingdom regulators.
Ofcom chief executive Sharon White has said she is "absolutely confident" that the broadcasting regulator was right in ruling that the planned purchase of Sky by Rupert Murdoch's 21 Century Fox would not undermine its broadcasting standards.
Competition and Markets Authority or CMA announced Tuesday, regarding its investigation into the proposed takeover of Sky Plc by 21st Century Fox, that it will now examine how the deal would impact media plurality and broadcasting standards in the UK.
"Are you confident that the CMA won't unearth new Fox scandals which derail the bid?", Alaphia Zoyab from activist group Avaaz asked.
Sky is also set to update the market with results for the three months to 30 September on Thursday.
It reported that the first series of home-grown drama Riviera achieved 20 million downloads, becoming its highest ever rated Original commission and Game of Thrones became the most watched series ever on Sky.
Sky CEO Jeremy Darroch, Fox CFO John Nallen and former Fox no. 2 Chase Carey were also among those board members re-elected on Thursday, each with more than 98.5 percent of the shareholder vote in their favor.
He said the company was seeing good demand for its flagship Sky Q product as well as for its streaming service Now TV.
Shares in 21st Century Fox were flat at $25.50 in light-volume trading.
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