The two substitutions means Kansas City will be sending 10 players to Hawaii.
Bowman tore the anterior cruciate and medial collateral ligaments in his left knee in Sunday's NFC championship loss to Seattle. Brady bowed out of the all-star game one day after New England lost to Denver in the AFC championship.
This will be Johnson's third straight Pro Bowl, while Smith will be headed to his first.
They'll be joined in Hawaii by Chiefs left tackle Branden Albert, safety Eric Berry, running back Jamaal Charles, cornerback Brandon Flowers, defensive tackle Dontari Poe, punt returner Dexter McCluster and linebackers Tamba Hali and Justin Houston.