The NFL announced the changes on Wednesday. Brady and the rest of the New England Patriots had physicals after their 33-14 opening-round playoff loss to Baltimore on Jan. 10.
Brady played in all 16 regular-season games and completed 371 of 565 passes for 4,398 yards, 28 touchdowns and 13 interceptions. His completion percentage of 65.7 was seventh in the NFL and his passer rating of 96.2 was ninth.
Schaub, selected to his first Pro Bowl, completed 396 of 583 passes for 4,770 yards, all the most in the NFL. He ranked fourth with a 67.9 completion percentage and seventh with a 98.6 passer rating. He threw for 29 touchdowns, including the game-winner in Houston's 34-27 victory over New England in the final regular-season game, and 15 interceptions
Smith led the NFC and shattered the Giants' single-season record with 107 catches in 2009, and his 1,220 receiving yards were the second-highest total in club history.
"I'm really excited about playing in the Pro Bowl," Smith said. "It's truly an honor to be recognized by the fans, coaches and players as one of the best in the league. I realize how significant it is at the position I play, by being the first Giants wide receiver to be named to the Pro Bowl in such a long time. I plan to represent my teammates, my coaches and the entire Giants organization well, because I know I would not have made it without their support."
Brady was chosen for his fifth Pro Bowl but withdrew for the second consecutive time. Patriots wide receiver Wes Welker, who suffered a serious knee injury in the regular-season finale at Houston, was also voted to the AFC roster and initially was replaced by teammate Randy Moss. Then Moss withdrew with an injury and was replaced by Cincinnati Bengals receiver Chad Ochocinco.
The Associated Press contributed to this report