The 87-year-old died on Sunday night after a battle with motor neurone disease.
Mr Cowley spent more than 40 years at News Corporation as one of Mr Murdoch's most trusted executives, including around two decades as head of the media company's Australian operations.
He also bought iconic bootmaker RM Williams in the early 1990s before selling down his stake in 2013.
A statement from Mr Cowley's son, Matt, paid tribute to his father and thanked people for their kind words and fond memories.
"He was not just a magnificent business mind but an amazing loving dad and husband to my mum for 64 years," he said.
"He was my dad, best friend and just an amazing man to everyone he met."
Matt Cowley listed some of his father's achievements, including helping to establish The Australian newspaper and assisting RM Williams in building the Australian Stockman's Hall of Fame and Outback Heritage Centre.
"Most of all he was ... Maureen's husband. He will be missed by many but remembered fondly," he said.
Mr Cowley was also a pivotal player in the 1990s News Corp-led push to establish Super League, a Murdoch-backed rival to the Australian Rugby League and its supporter Kerry Packer.
He was appointed an Officer of the Order of Australia in 1988 and was awarded an honorary doctorate from the University of New South Wales in 2008.
Mr Cowley retired from the News Corporation board in 2011 after 32 years a director of the company.
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