Brady is out after playing through rib and finger injuries late in the season. Patriots Coach Bill Belichick had downplayed the seriousness of Brady's injuries.
Brady, the sixth-round pick by New England in the 2000 NFL Draft, amassed 4,398 passing yards with 28 touchdowns and 13 interceptions after missing the 2007-08 season with a serious left knee injury.
Schaub originally was a second alternate because Pittsburgh's Ben Roethlisberger bowed out due to a right shoulder injury.
Schaub's career-best 4,770 yards this season led the NFL, and the Texans finished 9-7, the first winning season in franchise history.
He joins Houston teammates wide receiver Andre Johnson, defensive end Mario Williams and linebackers DeMeco Ryans and Brian Cushing on the AFC squad.
In other Pro Bowl roster moves Wednesday, Tennessee quarterback Vince Young was named to replace San Diego's Philip Rivers, whose wife will be soon be delivering their fifth child, and San Francisco running back Frank Gore will play in the game in place of Steve Jackson of St. Louis.
Both Young and Gore will be making their second Pro Bowl appearances. The game will be played in Miami on the Sunday prior to the Super Bowl.