He also played a major role in the Nix's run to the semifinals of the FFA Cup, deputising at centre back in their dramatic quarter-final win over Melbourne City.
Phoenix head coach Ufuk Talay says it's a major disappointment for Rufer and the team.
"We really feel for Alex as he has been playing some of his best football in recent weeks," Talay said.
"It's also a major setback for the team to lose their captain midway through the season.
"Alex has grown into a fantastic leader and will be missed, but it's an opportunity for other players to step up in his absence."
Rufer will be particularly missed this week, with Ben Old, Ben Waine, Clayton Lewis and Oli Sail away with the All Whites for international duty at the OFC Fifa World Cup qualification tournament, while David Ball is suspended after picking up his fifth yellow card for the season.
The Wellington Phoenix will have a new captain for Friday night's match against the Newcastle Jets with vice-captain Sail in Qatar with the All Whites.