The Argentinian, who has committed to the Victory for two years, won the Johnny Warren Medal as the A-League's best player in 2010-11, his only previous season in Australia.
He has since played with Chinese club Henan Jianye, who released him in June.
Flores will be the Victory's international marquee player, filling the club's last slot for an overseas signing.
Coach Ange Postecoglou said he knew from experience coaching against Flores during his previous A-League season what a threat the 26-year-old could be.
"Marcos is the type of player you don't really want to come up against as an opposition coach," Postecoglou said.
"Having him on board with us now will be really exciting, not only for the club but for our fans also."
Postecoglou said it was a sign of Flores' quality that he had such a big impact in his first season in the A-League, given it normally took foreign players time to adapt.
Flores said it was an exciting time to be joining the Victory, with Postecoglou and a group of new players arriving.
"Victory have many great players and I'm looking forward to getting to know everyone better," he said.