Manning threw for 400 yards and two touchdowns Sunday to lead Denver to its first trip to the NFL title game in 15 years.
The Broncos (15-3) will play Seattle on Feb. 2 at MetLife Stadium in East Rutherford, N.J.
It marks the next big step for Manning on a comeback from multiple neck surgeries that almost ended his career.
He led the Broncos on a pair of 7-plus-minute touchdown drives, the second of which gave Denver a 20-3 lead.
Manning improved to 5-10 lifetime against Brady but is now 2-1 in the AFC title games.
The Patriots (13-5) got only 64 yards rushing and most of Brady's 277 yards came after New England had fallen behind by 20.
SEAHAWKS 23, 49ERS 17
SEATTLE (AP)—Russell Wilson threw a 35-yard touchdown pass on fourth down and Seattle's top-ranked defense forced two late turnovers, lifting the Seahawks into their second Super Bowl with a victory over San Francisco for the NFC championship.
Seattle will meet Denver for the NFL title in two weeks in the New Jersey Meadowlands. It's the first trip to the big game for the Seahawks (15-3) since they lost to Pittsburgh after the 2005 season.
The conference champs had the best records in the league, the first time the top seeds have gotten to the Super Bowl since 2009.
San Francisco (14-5) led 17-13 when Wilson, given a free play as Aldon Smith jumped offside, hurled the ball to Jermaine Kearse, who made a leaping catch in the end zone.
Steven Hauschka then kicked his third field goal, and Seattle intercepted in the end zone on the 49ers' final possession.
AP NFL website: http://www.pro32.ap.org