The Argentine is expected to undergo reconstruction surgery on his right knee for the injury suffered in training on Thursday.
Friday's diagnosis means the Mariners are certain search for a quality replacement in the January transfer window.
It comes at an especially bad time as fellow Mariners playmaker Michael Glinchy is due to play his last game for the club on Sunday before heading off to join former Mariners coach Graham Arnold at his Japanese club.
Mariners coach Phil Moss vowed the team would maintain a stern title defence despite the latest blow.
"It is a bitter blow for Marcos and for the club," said Moss.
"Over the coming months we will do whatever we can to help Marcos in his recovery and return to the game.
"Despite the loss of Marcos for this season we will continue to show that we are made of tough stuff here at the Mariners.
"We have the quality and the mental strength to continue moving in the right direction."