They will face Seattle in Super Bowl XLVIII after the Seahawks edged San Francisco in Sunday's other conference title game.
Manning will be playing in his third Super Bowl, where he is 1-1 in two appearances with the Indianapolis Colts.
Thomas finished with seven catches for 134 yards, Julius Thomas added eight grabs for 85 yards and Eric Decker chipped in five receptions on his way to 73 yards for Denver.
On defense, the Broncos sacked New England's Tom Brady twice and held the Patriots to 64 rushing yards.
Brady went 24-of-38 for 277 passing yards with a passing and a rushing touchdown as New England dropped a second AFC title game in two years.
Julian Edelman made 10 catches for 89 yards for the Patriots.