The Ravens made up for the loss to the Patriots in last year's American Football Conference championship game in Foxboro by rallying in the second half as Flacco carved up the New England defence.
Baltimore advances to their first National Football League championship contest since the 2000 season and will face San Francisco, who also won on the road on Sunday, beating the top seeded Atlanta Falcons 28-24 in another come-from-behind thriller in the National Conference title game.
The win means Ravens veteran Ray Lewis will cap his career with a Super Bowl appearance. And two brothers will coach against each other in Super Bowl 47.
John Harbaugh's Ravens will square off against his brother Jim's San Francisco team on February 3 in New Orleans.
Flacco sliced up the Patriot's defence by throwing three touchdown passes after halftime, as the Ravens scored 21-consecutive points at Gillette Stadium. Flacco completed 21-of-36 passes on the game.
Anquan Boldin caught two of Flacco's touchdown passes and Ray Rice ran for a TD.
Tom Brady set the all-time NFL record for career playoff yards, but he couldn't get the job done when it mattered the most as the Ravens denied New England a record-tying eighth Super Bowl berth.
Brady completed just 29-of-54 passes for 320 yards with two interceptions. He had one touchdown pass to Wes Welker.
One of the key turning points was when New England's Steven Ridley took a huge hit to the helmet from Baltimore's Bernard Polland and fumbled the ball away in the fourth quarter.
Ridley immediately went to the dressing room for medical treatment and didn't return.
A New England offence that had averaged nearly 35 points per game in the regular season punted the ball five times on Sunday, including three inside Baltimore territory.
Baltimore defeated the New York Giants 34-7 in their only other Super Bowl appearance.
Earlier, in Atlanta, Frank Gore had a pair of touchdown runs in the second half as the 49ers stormed back from a 17-point deficit to beat the Falcons 28-24 and advance to the NFL championship game for the first time since 1995.