Allen, drafted with the second-round pick Philadelphia acquired from Washington in the Donovan McNabb trade, is the fourth defensive starter to go down for the season.
A potential fifth, middle linebacker Stewart Bradley, is out with a dislocated elbow and may not return until the playoffs.
Allen was hurt in the Eagles' 38-31 win over the New York Giants. His knee appeared to buckle while he tackled Mario Manningham.
He'll join rookie defensive end Brandon Graham and cornerback Ellis Hobbs on injured reserve. Rookie Kurt Coleman, a seventh-round pick, takes Allen's starting spot.