New coach Ufuk Talay confirmed Marinovic would be his first player acquisition since succeeding Mark Rudan last month, although talks with the well-regarded 27-year-old have been under way for a longer period.
Marinovic replaces Polish gloveman Filip Kurto, who enjoyed an excellent single season in Wellington. Kurto was crowned A-League goalkeeper of the season before announcing his departure for the Rudan-coached Western United.
The Phoenix have suffered further player losses since, including club record goal-scorer Roy Krishna, but Talay was delighted to unveil Marinovic, who has played 24 times for the All Whites.
''For us, he'll be an exceptional leader inside the box and a great shot stopper as part of our backline," Talay said.
''To have Stefan's international pedigree will further add to our number of talented homegrown players within the club."
Marinovic arrives from English Championship club Bristol City, having previously made 100 appearances at various club levels in Germany before a stint with Major League Soccer outfit Vancouver Whitecaps.
After a decade away from New Zealand, Auckland-born Marinovic was relishing a return home and linking with Phoenix goalkeeping coach Paul Gothard, who has been involved with the All Whites.