The Marlins announced the move after beating the Pittsburgh Pirates 7-3.
The Phillies had designated Helms for assignment on Wednesday, and had 10 days to either trade him or put him on waivers. The 31-year-old Helms, who opened last season as the starting third baseman for Philadelphia, is due $2.9 million this season.
"He's a scrapper, a great clubhouse guy," Marlins second baseman Dan Uggla said. "Wes is a veteran who can do a lot of positive things for a team. He can bring a lot to a young team like this."
To make room for Helms, the Marlins designated Jason Wood for assignment.
Jorge Cantu has been starting at third base for the Marlins so far this season.
Helms batted .246 with five homers and 39 RBI in 280 at-bats last year in Philadelphia.