The Yankees announced the roster move before Tuesday night's series-opening 6-3 loss to the Mets.
Stanton requested an MRI on Monday after he woke up with a sore Achilles, but Yankees manager Aaron Boone said Tuesday he had been in communication with the slugger about the normal wear and tear of the season that predated the All-Star Game. Boone said Stanton's Achilles flared up after the break for the Midsummer Classic.
"Hoping it's a minor thing," Boone said.
Stanton started his treatment on Tuesday, and the Yankees' medical staff will check in on the Achilles in a week. Boone said the time frame for return is around two to three weeks but could be sooner. Additionally, Stanton will take a break from baseball activities for about 10 days.
Stanton was out of the starting lineup for New York's past two games against the Baltimore Orioles this past weekend.
Stanton, 32, is batting .228 with 24 home runs and 61 RBIs this season for the first-place Yankees.
The Yankees recalled outfielder Tim Locastro from Triple-A Scranton/Wilkes-Barre to replace Stanton on the roster.
ESPN's Joon Lee contributed to this report.