Popovic, 39, signed a reported four-year deal in the fledgling team's first announcement as it prepares to enter the national league in the 2012/13 season, kicking off in October.
Popovic was this week formally released as assistant coach of English Championship club Crystal Palace to take up the role in one of Australia's great football nurseries.
It is Popovic's first head coaching job since assistant coaching roles with Sydney FC and Crystal Palace and follows a 19-year playing career with Japan's Sanfrecce Hiroshima, Crystal Palace, Qatar's Al Arabi, Sydney United and Sydney FC.
Popovic's major task will be building the new Sydney club's squad from scratch, with the team's name, colours, home ground and coaching staff still to be decided five months out from next season.
Popovic was capped 61 times for Australia in 12 years and was part of the Socceroos squad at the 2006 FIFA World Cup™ in Germany.
"I'm definitely excited, I'm honoured, privileged," Popovic said at the official announcement. "Certainly it's a great challenge, but one that I can handle.
"Hopefully I'll bring a lot of leadership. Knowing the area, growing up in the area, I know what the people of the region expect," he said.
Lyall Gorman, who was involved in the set up of established A-League club Central Coast Mariners, was also appointed executive chairman of the new Sydney club.