Infielder Brian Anderson also went on the IL with lower back spasms for the Marlins, who went 7-19 in May.
Wendle aggravated the hamstring in the same spot while sliding into second base in the fourth inning of Monday's 7-1 loss against the Rockies. Wendle first missed three games in early May with the injury, then returned for seven games before going on the IL on May 12.
Wendle, a first-time All-Star last season with Tampa Bay, was back in the lineup Friday and went 1-for-10 in four games. He singled Monday and was removed after moving to second on a grounder.
"I know Joey is frustrated, feeling like he did everything right," manager Don Mattingly said. "We kind of took our time with him. We felt like he was ready two or three days before he went out and played."
Wendle, whose stint on the IL is retroactive to Tuesday, was flying back to Miami and is expected to undergo tests Thursday. He's batting .284 with two home runs and 11 RBIs in 29 games.
"I don't think anybody feels that it's torn off the bone or anything, it just, more of it continues to happen," Mattingly said. "You see a guy that really does a hammy in a bad way, they can hardly walk. He walks fine. You don't feel like it's major, major, but hamstrings are rough."
Mattingly had more confidence that Anderson will be ready to return when he's eligible to come off the IL on Tuesday.
"Andy, I think, is probably in a better spot than Joey right now," Mattingly said. "It kind of puts him back in the mix if we can get him over the hump."
The latest injuries are another blow to the Marlins, who have struggled after starting 12-8. They entered Wednesday 19-27 and 12½ games behind the NL East-leading New York Mets.
"Joey's one of our best hitters. Brian Anderson is one of our best hitters," catcher Jacob Stallings said. "I don't know if it affects the overall team consistency, but they're really good players."