Pignata today announced his resignation after three years in the job.
He leaves the club next Friday, with the role being filled in the interim by the club's head of commercial operations, Nathan Greenham, before a search is made for a fulltime replacement.
Pignata said his decision was prompted by a desire to return to Melbourne to be with his family.
"It's been the toughest decision I've had to make, to be honest, but it came to a point where I had to make a decision between the family I love and the job I love, and family always comes first for me," said Pignata, who joined the club shortly after its inception in 2007.
"It's going to be sad leaving the Phoenix, saying goodbye to the players and staff was very hard for me.
"But it's been very difficult being apart from my wife and two sons, who went back to Melbourne six months ago, and it simply became too tough to commute back and forth."
Pignata said he believed he was leaving the Phoenix in a sound position, from both a financial and on-field point of view.
Pignata said the Phoenix's 2009-10 campaign, when they reached the last three, had been the highlight of his three years in Wellington.
"No other New Zealand-based club had ever made the playoffs in the A-League -- we went within one match of being in the grand final.
"We proved the naysayers wrong on both sides of the Tasman about the standing of football in New Zealand and that's immensely gratifying."
Pignata said the Phoenix had a bright future, having recently secured a five-year A-League license extension.
"From a club perspective we're in top shape both on and off the field."
Phoenix owner Terry Serepisos praised Pignata's contribution to the club.
"Tony achieved things for the Phoenix that I think only he had the ability, expertise and commitment to deliver. He has worked tirelessly since coming to the club and I know it's been difficult for him since his wife and sons went back to Australia."
