To fill their spots, the Padres selected the contract of infielder James Darnell and recalled left-hander Wade LeBlanc from Triple-A Tucson. LeBlanc is scheduled to start Tuesday night.
Headley leads the last-place Padres with a .380 on-base percentage, 28 doubles and 43 RBIs. He was hurt while sliding headfirst on a stolen base Saturday night in Pittsburgh.
Logan Forsythe started at third base for the second consecutive game.
The 24-year-old Darnell was batting .317 with 23 homers and 75 RBIs in 102 games between Double-A San Antonio and Tucson this season. He was chosen for the Futures Game during All-Star week.
The Padres began the day last in the majors with 63 home runs. They were batting .235, worst in the NL. Still, they arrived in New York on an offensive tear that had keyed a four-game winning streak.
Headley was put on the DL retroactive to Aug. 6, and Frieri retroactive to Aug. 5.
San Diego also transferred outfielder Brad Hawpe from the 15-day disabled list to the 60-day DL. Hawpe had Tommy John surgery on his left elbow.
LeBlanc is slated to pitch in place of right-hander Dustin Moseley, who had season-ending surgery last week on his non-throwing shoulder. Moseley dislocated his left shoulder while hitting a single July 26.