The move was announced shortly after the Mets began their series finale with the Chicago White Sox and is retroactive to Monday.
Marte was not in the lineup for the fourth time in five games, though manager Buck Showalter said before the game that the veteran is feeling better. On Wednesday afternoon, Marte saw a specialist and underwent a scan. The Mets, who began Thursday at 45-50, did not announce a corresponding move to replace Marte.
The Mets also lost left fielder Tommy Pham who exited Thursday's game after suffering a right groin injury while grounding into a double play to end the third inning.
Pham, who was 0-for-2, went out to left to start the fourth inning but jogged back to the dugout shortly thereafter.
Despite feeling some tightness in his groin, Pham is optimistic he can avoid a stint on the injured list.
"I don't want to give out false hope and say something and have to retract my words but I would say it's not as bad as two weeks ago, so there's reason to be optimistic," said Pham.
In the second season of a four-year, $78 million contract, Marte is batting .254 with five home runs, 28 RBIs and 24 stolen bases in 84 games. Last season, Marte hit .292 with 16 home runs and 63 RBIs to go along with 18 stolen bases in 118 games.
Pham, 35, is batting .272 with nine homers and 35 RBIs in 74 games in his first season with the Mets.
The Associated Press and Reuters contributed to this report.