Waugh becomes the first Wallaby to occupy the role, having earned 79 caps for the national side.
Since he concluded his professional career with the Waratahs in 2011, Waugh has gone on to build extensive executive and governance experience.
He has been a non-executive director on the Rugby Australia board since July 2018, and he has most recently had a career in banking.
Waugh's Board and governance experience has seen him hold multiple non-executive directorship positions within the hospitality, finance and sporting industries.
Rugby Australia Chairman Hamish McLennan said the board were impressed with Waugh's vision for the game, his experience across a range of sectors, and his in-depth understanding of Australian Rugby.
"'Waughy' has proven himself on and off the field as a true believer in the potential of where the global game of rugby can take you.
"Phil has exacting standards which will deliver us improved pathways and success as we prepare for the Golden Decade of Rugby ahead for our men, women, boys and girls.
"We are on a mission and Phil will make sure we get there."
Waugh's illustrious playing career began with the Narrabeen Tigers on Sydney's northern beaches, before he went on to play First XV in his final three years at Shore school, and going on to play for Australian Schoolboys in 1996 and 1997.
The openside flanker played for the Australian Under-19s and Under-21s, and made his debut for the NSW Waratahs as a 19 year-old in 1999. He went on to play 136 caps for the Waratahs and retired in 2011 as the club's most capped player and captain.
Waugh played at two Rugby World Cups for the Wallabies (2003 and 2007), was the John Eales Medallist in 2003, and became the Wallabies' 74th Test captain in 2006.
A Warringah Rats junior, Waugh spent his Club Rugby days at Sydney University.
Waugh is invigorated by the opportunities that lie ahead for the game in Australia.
"Above all, the role comes with enormous responsibility to ensure our great game thrives throughout communities across Australia," Waugh said.
"Our priority will be to develop the game from the grassroots to the elite level - both in Australia, and with our partners across the Pacific.
"We need to align our professional pathways, and work as one team from club to country, with the goal of being the best and most successful men's and women's rugby systems in the world.
"Having put my heart and soul into the game on the field in my playing days, I intend to put the same level of passion and commitment into the game as Rugby Australia CEO."
Waugh will commence his new role on 6 July.