Lynch carried the ball 22 times and ran for a 40-yard touchdown early in the second half, which erased a 10-3 halftime deficit.
With Seattle trailing 17-13 early in the fourth quarter, Russell Wilson connected with Jermaine Kearse on a 35-yard scoring strike, putting the Seahawks ahead to stay.
Steven Hauschka booted a 47-yard field goal with 3:43 left for a six-point lead, and Malcolm Smith intercepted a Colin Kaepernick pass in the end zone with 22 seconds remaining to secure the Seahawks' victory.
They will face AFC champion Denver Feb. 2 in Super Bowl XLVIII. The Broncos downed New England in Sunday's other conference title game.
Wilson completed 16-of-25 passes for 215 yards. Doug Baldwin led Seattle's receiving corps with six catches for 106 yards.
Kaepernick ran for 130 yards on 11 carries but lost a fumble and was intercepted twice for the defending NFC champion 49ers.
He was limited to 153 passing yards 14-of-24 efficiency.