Shepherd was carted off the field after colliding with running back Darren Sproles during practice on Sunday, just over a week after the Eagles announced they had traded three-year veteran cornerback Brandon Boykin to the Steelers for a 2016 draft pick.
The Eagles selected three cornerbacks in the 2015 draft: Shepherd (sixth round), Eric Rowe (second round) and Randall Evans (sixth round). Shepherd had been undergoing the most reps of the three rookies at the position.
Jaylen Watkins, a fourth-round pick in 2014, is slated to take Shepherd's place at nickel cornerback.
Philadelphia signed No. 1 cornerback Byron Maxwell to a six-year, $63 million contract this off-season.
The Eagles play their first preseason game against the Colts on Sunday.
- Erin Flynn