On January 6, 2013, in the Wild Card Playoffs round against the Indianapolis Colts, Flacco finished the game 12 of 23 for 282 yards, two touchdowns, and a career postseason high 125.6 passer rating. The 24–9 win at home set up a Divisional round rematch with the Broncos, who entered the game as nine-point favorites after their regular season win over the Ravens, which included a 98-yard interception touchdown return by Broncos' cornerback Chris Harris that marked the lowest point of Flacco's season. Continuing his postseason success, Flacco played one of the best games in his career, throwing for 331 yards and 3 touchdowns. In the fourth quarter, the Ravens were down 35–28 and had one last chance to tie the game. After an incomplete pass and a 7-yard scramble, on 3rd down and 3, Flacco heaved a 70-yard touchdown pass to Jacoby Jones, sending the game into overtime. The pass has been called the "Mile High Miracle", and "one of the greatest plays in NFL history" and drew comparisons to Roger Staubach's "Hail Mary", Terry Bradshaw's "Immaculate Reception", and Joe Montana's "The Catch". The Ravens would go on to win the game in double overtime 38–35 after an interception by Corey Graham from Peyton Manning and a 47-yard field goal from Justin Tucker, sending the Ravens to face the New England Patriots in the AFC Championship for a second straight year.
On January 20, 2013, Flacco and the Ravens avenged the previous year's AFC Championship Game loss to the New England Patriots with a 28–13 win, securing their spot in the 2013 Super Bowl. Flacco threw for 240 yards and three touchdowns, notching his third straight game with a passer rating over 100. With this win, Flacco became the second NFL quarterback to defeat both Peyton Manning (with the Broncos) and Tom Brady in the same postseason since both became starting quarterbacks in 2001 (the first to do so was Mark Sanchez in 2010).
On February 3, 2013, the Ravens met the San Francisco 49ers in Super Bowl XLVII. The 49ers were a 4-point favorite to win the game, but Flacco completed 22 of 33 passes for 287 yards and three touchdowns, to lead the Ravens to a 34-31 win. Flacco’s three touchdowns in the game tied him for first place on the list of most consecutive playoff games with at least three touchdown passes (3 games). With a record fourth playoff game with a 100+ passer rating in a single postseason, Flacco was named the game's Most Valuable Player, and was awarded a brand-new 2014 Chevrolet Corvette.
On March 4, 2013, Flacco became the highest-paid quarterback in NFL history when he signed a six-year contract worth $120.6 million. However, within months, he was surpassed by the Packers' Aaron Rodgers and the Falcons' Matt Ryan.
Flacco's 2013 season was statistically the worst of his career. For the first time as an NFL quarterback, Flacco threw more interceptions than he threw touchdowns. His 22 interceptions in the season were 10 more than he had thrown in any other season. His 19 touchdowns were also his lowest since his rookie year. His passer rating was a career low 73.1, approximately 7 points lower than Flacco's previous worst season passer rating. He was also sacked more times (48) than he was in any other season in his career. Despite all this, he also set a high in passing yards, with 3,912. The Ravens finished 8–8 for the season and Flacco missed the playoffs for the first time in his career. He was ranked 58th by his fellow players on the NFL Top 100 Players of 2014.
Flacco is the oldest of the five boys in his family. His brothers are named Mike, John, Brian, and Tom, and he also has a sister named Stephanie. His brother Mike was selected in the 31st round of the 2009 Major League Baseball draft by the Baltimore Orioles, and was the starting first baseman for the Frederick Keys, who won the 2011 Carolina League championship. He hit for a .250 average, with 5 HRs and 22 RBIs in 50 games with the Keys. The Orioles traded him to the Boston Red Sox on March 15, 2013, and rather than accepting the assignment, Flacco decided to retire from baseball. He then enrolled at the University of New Haven to play football as a tight end, and declared for the 2014 NFL Draft. Another brother, John, was a walk-on receiver with the Stanford Cardinal football team and played against the Army Black Knights football team at the 2013 Stanford vs. Army football game. Joe's youngest brother, Tom Flacco, enrolled in 2015 at Western Michigan University, where he played quarterback for two seasons before transferring to Rutgers in 2017 and then Towson in 2018.