Seattle, who boast the best defence in NFL, forced three turnovers in the fourth quarter to beat San Francisco 49ers 23-17 in the National Conference final while Manning led the Broncos over the New England Patriots 26-16 in the American Conference final.
After sharing the NFL's best record at 13-3 in the regular season, the Broncos and Seahawks will meet in Super Bowl 48 on February 2 in suburban New York.
It will be Denver's seventh trip to the Super Bowl and the second visit for the Seahawks, who lost to Pittsburgh in 2006.
"This feels even sweeter," Seahawks owner Paul Allen said.
The Seahawks trailed until the fourth quarter, when Russell Wilson connected with Jermaine Kearse on a 35-yard touchdown pass to put Seattle ahead to stay and the hosts took away the ball from the 49ers three times.
"This is really special," said Seahawks coach Pete Carroll. "This team was ready to finish. They knew we weren't in the lead. That didn't matter. They were going to come out here and do what they needed to do."
Manning completed 32-of-43 passes for 400 yards and two touchdowns.
"It's very rewarding when you put in so much hard work and it pays off with the win in a big game," Manning said.
"We've kept our nose to the grindstone, kept persevering and it feels great to get this win."
New England's Tom Brady leads the all-time rivalry with Manning 10-5 but fell to 2-2 in their play-off meetings.
"We just didn't make enough plays," Brady said. "We dug a pretty big hole and they played really well ... They were certainly the better team today."
The 49ers, who lost last year's Super Bowl to Baltimore, saw their hopes end on Malcolm Smith's interception with 22 seconds remaining.
"It was a 15-round fight," 49ers coach Jim Harbaugh said. "It was a great fight by our guys ... A man can be destroyed. He can't be defeated."
Broncos coach John Fox, who underwent heart surgery in November and steered Carolina to the Super Bowl 10 years ago, said: "I couldn't be prouder of a group of men in my life."
Denver's Matt Prater kicked four field goals while Manning flipped touchdown passes of 1 yard to Jacob Tamme and 3 yards to Demaryius Thomas.
The Patriots fell behind 13-3 at half-time and Brady struggled most of the day against Denver's defenders.
New England pulled within 13 points on Brady's 7-yard touchdown pass to Julian Edelman with 9:26 remaining but Prater added a 54-yard field goal for a 26-10 Denver edge.
Brady scored on a 5-yard run with 3:07 to play, but Denver's defence stopped Shane Vereen's 2-point conversion run attempt to create the final margin and the Broncos ran out the clock from there.
At Seattle, the 49ers took a 10-0 lead on Phil Dawson's 25-yard field goal and a 1-yard Anthony Dixon touchdown plunge that was set up by a 58-yard run by quarterback Colin Kaepernick.
Kaepernick drove the 49ers toward a potential winning touchdown late in the game but Seattle's Richard Sherman, who led the NFL with eight interceptions, deflected a pass into Smith's hands to end the threat.
"That's as sweet as it gets," Sherman said. "We knew we had to finish it off."