Mathis is unable to play in the NFL's all-star game in Miami on Sunday because he'll be preparing for the Super Bowl against New Orleans the following week. Mathis is one of seven Colts players being replaced on the Pro Bowl roster.
Ellis will play in his second Pro Bowl, and first since the 2003 season, despite having a broken left hand that requires surgery.
Ellis had 6½ sacks during the regular season and ranks third in franchise history with 68 sacks. He joins cornerback Darrelle Revis, left guard Alan Faneca, center Nick Mangold and left tackle D'Brickashaw Ferguson as Jets in the Pro Bowl.