The 30-year old Costa Rican midfielder has signed a two-year deal with the New Zealand club but will not join until his current deal with Indian outfit Prayag United expires in June.
"I've always had a good relationship with Carlos and from the first call I made to him our talks were positive," said Phoenix coach Ricki Herbert said.
"Getting Carlos to Wellington is a massive signing for Phoenix because everyone has seen the impact he made in the A-League.
"He is an exciting player who can make things very difficult for the opposition and is a dead ball specialist.
"It was important that when a player of Carlos's ability became available that the club should try and get him here.
"It signals the direction the club is taking and Carlos fits perfectly with our strategy.
"The fact that he has been A-League player of the year says it all as that is voted on by his peers.
"I'm delighted Carlos has decided to continue his career with Phoenix and I am looking forward to working with him."
Hernandez scored 40 goals in 138 appearances for the Victory during his time there which yielded the 2008-09 A-League Championship/Premiership double, the 2009-10 Johnny Warren Medal and the 2009-10 Victory Player of the Year.