Bertos, 32, has had an injury-interrupted season after becoming a fan favourite on joining the Phoenix in 2008 and playing 127 times for the club.
Huysegems, 31, has been with the club for the past two seasons and was its leading scorer this season with 10 goals.
"Leo is a Wellington, Phoenix and New Zealand footballing legend," coach Ernie Merrick said.
"This year has been tough for Leo, starting with injuries before the season even began.
"It meant he never got to the levels of fitness he is used to as he has always been an extremely fit player.
"Ironically he had an operation a few weeks ago and now that the season is ending is probably in the best shape he has been all year."
Merrick described Bertos as a great character who mentored the club's young players, and was part of a Phoenix leadership group that had been exceptional.
"It is a great regret that he is leaving, but if he continues playing I know he will do well because one of the most important parts of his make-up is that he never gives you less than 100 per cent," Merrick said.
"His injuries prevented him playing his best football while I've been here, but I know what he is capable of from when he has played against my team in the A-League both for Wellington and Perth.
"I'm sure he will remain part of the All Whites set up and whatever eventuates in the next couple of years it would be great to see him back at the Phoenix in some capacity."
Merrick describes Huysegems as the ultimate professional, going so far as to say he is "probably the most professional footballer I have worked with".
"Despite his experience he is always willing to learn," the coach said.
"He worked hard to fit into the style of football we wanted to play.
"Stein has been an integral part of the team this season and is our top goal scorer.
"He is a great character as well as a very good person.
"It is sad to see him go but that is the nature of football. I know Stein will be a very competitive player wherever he ends up and if we have to face him expect him to give us a tough time"
"He has been a pleasure to work with and I'm sure he will continue to score goals wherever he goes, just hopefully not against us!"
New Zealand Herald