The 47-year-old replaces Dirk Melton who was abruptly sacked by the club in March for behaviour described as "completely unacceptable".
Pignata spent three years at the helm of Football Federation Victoria prior to heading up the Phoenix since the club's inception in 2007 before resigning in June 2010.
The Australian businessman also has 20 years experience in the finance industry.
Pignata's appointment is the latest in a number of new names at the revamped club with Russian millionaire David Traktovenko becoming the majority owner earlier this month and youth league coach Ian Crook promoted to the head coaching role.
Traktovenko's son-in-law Scott Barlow, who was this month installed as the club's chairman, feels Pignata is an ideal acquisition for the Sky Blues.
"Tony has a proven track record of successfully managing an A-League club and a state federation as well as a wealth of commercial acumen gained from his background in the banking and finance industry," Barlow said.
Pignata is excited about the challenges of taking on one of the most demanding roles in football.
"Sydney FC is one of the flagships of the A-League and it will be a privilege to work at such a strong club at what is a very exciting time in the evolution of the competition," Pignata said.
"It's great to be back in football, which is my passion."
Pignata will officially take on the role on June 12.