After becoming the first team in NFL history to begin two consecutive seasons by winning at least their first 9 games, the Colts proceeded to lose 3 of their next 4 games, thanks largely to the league's worst run defense; however, they still capstured their 4th consecutive AFC South title by defeating the Bengals on MNF in Week 15 of the season with, ironically, a strong showing from their defense. The Colts finished the season with a 12-4 record, giving them the number 3 seed in the playoffs. The record also marked their fifth consecutive season with 10 victories or more. Also notable was that in week 13 against the Titans, QB Peyton Manning and WR Marvin Harrison became the first QB/WR combination in NFL history to complete 100 touchdown passes.

In the Colts' wild-card round playoff game, they defeated the Kansas City Chiefs 23-8, despite Peyton Manning's three interceptions. Shockingly, it was their defense that carried them, holding the Chiefs to 44 yards on the ground (Larry Johnson only had 32) and Chiefs' quarterback Trent Green to a meager 2 yards passing in the entire first half. The Chiefs didn't manage a first down until 3:33 remained in the third quarter.

The Colts defeated the Baltimore Ravens 15-6 in the division playoff round, thanks to kicker Adam Vinatieri's five field goals and another impressive defensive showing. They played the New England Patriots at home in the AFC title game for the rights to the Super Bowl; it was the Colts' third conference championship game in the Indianapolis era, but the first one played at home. The game also marked the first time the AFC title game was played in a domed stadium. After trailing at one point 21-3, the Colts stormed back to defeat the team that had done them in so many times 38-34. The 18 point comeback was the largest in NFL conference championship history.

On February 4, 2007, the Colts won Super Bowl XLI, defeating the Chicago Bears 29-17 in Dolphin Stadium, in Miami Gardens, Florida in the first-ever Super Bowl played in the rain. Rain was a substantial obstacle to both teams, as a combined total of six turnovers were recorded in the first half, a new Super Bowl high. Quarterback Peyton Manning, after a rocky start that saw him throw an interception, was named the MVP when he recovered to complete 25 of 38 passes, one for a touchdown. Reggie Wayne was the sole receiver of a passing touchdown from the Colts offense, and the running back duo of Dominic Rhodes and Joseph Addai combined for 190 yards, with Rhodes achieving the only rushing touchdown, and kicker Adam Vinatieri converted on 3 out of 4 field goal attempts. On the defensive side of the ball Pro Bowl safety Bob Sanders and cornerback Kelvin Hayden both intercepted Bears' quarterback Rex Grossman towards the end of the game, with Hayden returning his for 56 yards for a touchdown which helped seal the win for the Colts.

In winning the game Indianapolis became the first "dome team" to win a Super Bowl in an outdoor stadium as well as and the first to win in the rain. Tony Dungy became only the third man to have won the Super Bowl as both a head coach and a player (along with Tom Flores and Mike Ditka).

The Colts' logo and uniforms have basically remained the same since the team's official debut in 1953. The helmet is white with a speed blue horseshoe logo. The blue jerseys have white shoulder stripes while the white jerseys have blue stripes. The team also wears white pants with blue stripes along the sides.

From 1982 through 1986, the Colts wore gray pants with their blue jerseys. The gray pants featured a horseshoe on the top of the sides with the player's number inside the horseshoe. The Colts continued to wear white pants with their white jerseys throughout this period, and in 1987, the gray pants were retired.

The Colts wore blue pants with their white jerseys for the first three games of the 1995 season, but they were discarded and the team returned to white pants with both the blue and white jerseys. The team made some minor uniform adjustments before the start of the 2004 season, including reverting from blue to the traditional gray face masks, darkening their blue colors from a light blue to speed blue, as well as adding two white stripes to the socks. In 2006, the stripes were removed from the socks.