The appointment comes on the same day that the underachieving club confirmed Tony Popovic's signing as new coach on a three-year deal.
Glory missed the 2017/18 finals after an underwhelming campaign under Kenny Lowe and are looking to return to the top of the domestic game in Australia after their NSL domination.
Pignata will take over from Peter Filopoulos who leaves Perth next week to take up the role as CEO at Football Federation Victoria (FFV).
The new Glory CEO has a decorated resume, having steered Sydney FC from 2012 to 2017, after a previous spell as inaugural Wellington Phoenix CEO from 2007 to 2010. Ironically he's also previously been FFV CEO.
Pignata played a key role in securing Alessandro Del Piero's services during his time at Sydney FC, while he also helped turn the club's culture as they did the double in 2016/17.
"I'm very proud and privileged to take up this role," Pignata said.

"WA has a rich football history, the club has great heritage and I'm really looking forward to working with Tony Sage and Tony Popovic to help Perth Glory fulfill its potential and to deliver success on and off the field."

Glory Owner and Chairman Tony Sage said: "Tony will be a massive asset to the club with his expertise, experience and track record of success and we look forward to working closely together."