Gaborik, 34, will miss the finals against Canada that begin Tuesday. He will also be out for the first part of the NHL season, which begins Oct. 12.
San Jose Sharks forward Mikkel Boedker will replace Gaborik in Team Europe's lineup.
Miroslav Satan, general manager of Team Europe, said Monday that Gaborik has left the team and will not return.
"Marian was a very important part of Team Europe throughout the entire World Cup of Hockey, and though he is leaving our group today, he remains a part of our team," Satan said in a prepared statement. "We know he will be supporting us in the final against Team Canada, and we wish him all the best in his recovery."
Gaborik scored a goal in Europe's upset win Sunday before taking a puck off his foot in the second period. He was seen on crutches with a walking cast on his right foot on Monday, according to multiple reports.
Team Europe coach Ralph Krueger said they will miss Gaborik's veteran experience against undefeated Canada.
"The impact will be that we're losing some leadership and some smarts on the puck that have really been exemplary for us," Krueger said Tuesday morning. "His character to play through the injury right through to score a goal against the Swedes is really part of the little pieces that this group is made of."
Boedker, 26, had been given a game off at the end of the pre-tournament schedule in part because he'd played an Olympic qualifying event with the Denmark national team.
"I think you've got to keep it simple and make sure you just make smart plays," Boedker said. "Obviously, Canada comes fast and they come strong, but to me it's all about just keeping it simple and just making sure I can help the team out any way possible."
ESPN Staff Writer Scott Burnside contributed to this report.