Allen, a rookie who has started every game this season, has a neck strain. Kurt Coleman, a rookie seventh-round pick, would replace Allen.
Jean-Gilles has a concussion. Nick Cole, who started the first three games at right guard, would take his spot.
Eagles coach Andy Reid says Jean-Gilles hasn't passed post-concussion testing yet.
Both players were injured in last Sunday's win against Indianapolis.
In other news, cornerback Ellis Hobbs returned to practice after missing a game with a hip injury.