Chicago Bears defensive end Julius Peppers also was chosen as a replacement for Giants defensive end Jason Pierre-Paul, who like Manning is bound for Super Bowl XLVI. It will be Peppers' seventh Pro Bowl in his 10-year career.
Newton was the first alternate among NFC quarterbacks after Manning, Green Bay's Aaron Rodgers and New Orleans' Drew Brees. The Giants' 20-17 overtime victory over the San Francisco 49ers in Sunday's NFC Championship Game made Manning unavailable for next Sunday's Pro Bowl in Honolulu and opened a spot for Newton.
Newton, the No. 1 overall pick in the 2011 draft, threw for 4,051 yards -- the most by a rookie in NFL history -- and 21 touchdowns with 17 interceptions this season. He added 706 rushing yards to become the first player in league history to pass for 4,000 yards and rush for at least 500 yards in a single season. Newton also set an NFL record for most rushing touchdowns by a quarterback in a single season with 14.
Newton was traveling Monday and unavailable for comment.
"The impact he has had on the organization and in the locker room, as well as the diversity he has brought to the offense has been enormous," Panthers general manager Marty Hurney told The Associated Press in a telephone interview from the Senior Bowl in Mobile, Ala. "He's been a huge spark at the most important position in the game right now. We're thrilled to see him get chance."
Peppers had 11 sacks this season, giving him 100 in his career. He's the sixth Bears player to be named to the Pro Bowl, joining cornerback Charles Tillman, running back Matt Forte and special-teamer Corey Graham, and linebackers Brian Urlacher and Lance Briggs. Urlacher and Briggs will not play in the game because of injuries.
The Associated Press contributed to this report.