It remains unclear how long he will be sidelined.
Beckham suffered his injury with about four minutes left in the fourth quarter. He fell awkwardly to the ground, and Chargers players immediately signaled to the sidelines for help.
Beckham had to be carted off the field.
He missed the Giants' season-opener against the Dallas Cowboys with an ankle injury, and after catching five passes for 97 yards on Sunday, Beckham has 25 receptions for 302 yards for the season.
He was the fourth Giants wide receiver to be injured Sunday.
Neither returned to the game.
In the second half, Dwayne Harris left on a cart with a fractured foot.
Shepard was the Giants' leading receiver coming into the game, with 21 catches for 254 yards and a touchdown. He had one reception for 9 yards on Sunday.
Marshall had two catches for 15 yards Sunday, giving him 18 receptions for 154 yards for the season.
Harris had no receptions Sunday.