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2001: Taking over as starter and first Super Bowl victory

With Bledsoe as the starting quarterback, the Patriots opened the 2001 season with a 23–17 road loss to the Cincinnati Bengals. In their second game and home opener on September 23, the Patriots squared off against their AFC East rivals, the New York Jets. Bledsoe was again the starter; in the fourth quarter, he suffered internal bleeding after a hit from Jets linebacker Mo Lewis. Bledsoe returned for the next series, but was replaced with Brady for the Patriots' final series of the game. New York held on to win 10–3, and the Patriots fell to 0–2 on the season. Brady was named the starter for the season's third game, against the Indianapolis Colts, in which the Patriots posted a 44–13 win.

In the Patriots' fifth game, Brady began to find his stride. Trailing the visiting San Diego Chargers 26–16 in the fourth quarter, he led the Patriots on two scoring drives to force overtime, and another in overtime to set up a winning field goal for a 29–26 victory. Brady finished the game with 33 of 54, for 364 yards and two touchdowns, and was named AFC Offensive Player of the Week for the first time in his career. The following week, Brady again played well during the rematch at Indianapolis, with a passer rating of 148.3 in a 38–17 win. Brady won his second AFC Offensive Player of the Week nomination after a four-touchdown day in a 34–17 win over the New Orleans Saints in Week 11. The Patriots went on to win eleven of the fourteen games Brady started, and six straight to finish the regular season, winning the AFC East and entering the NFL playoffs with a first-round bye. He finished the 2001 season with 2,843 passing yards and 18 touchdowns, earning an invitation to the Pro Bowl.

In Brady's first playoff game, he threw for 312 yards against the Oakland Raiders and led the Patriots back from a ten-point fourth-quarter deficit to send the game to overtime, where they won on an Adam Vinatieri field goal 16–13. A controversial play occurred in the fourth quarter of that game. Trailing by three points, Brady lost control of the ball after being hit by Raiders cornerback and former Michigan teammate Charles Woodson. Oakland initially recovered the ball but, citing the " tuck rule " – which states that any forward throwing motion by a quarterback begins a pass even if the quarterback loses possession of the ball as he is attempting to tuck it back toward his body – referee Walt Coleman overturned the call on instant replay, ruling it an incomplete pass rather than a fumble. Brady finished the game 32-of-52 for 312 passing yards and one interception.

In the AFC Championship Game against the Steelers, Brady injured his knee, and was relieved by Bledsoe. The Patriots won the game by a score of 24–17. Subsequently, Las Vegas oddsmakers positioned them as 14-point underdogs against the NFC champion St. Louis Rams in Super Bowl XXXVI.

Brady returned from his knee injury in the AFC Championship Game to start in the Super Bowl a week later at the Louisiana Superdome in New Orleans. Despite being heavy underdogs, the Patriots played well, holding the Rams' high-powered offense in check through the first three quarters. The Rams rallied from a 17–3 deficit to tie the game with 1:30 left in regulation. The Patriots then got the ball back at their own 17-yard line with no timeouts remaining. Sportscaster and former Super Bowl-winning coach John Madden argued that the Patriots should run out the clock and try to win the game in overtime. Instead, Brady drove the Patriots' offense down the field to the Rams' 31-yard line before spiking the ball with seven seconds left. Kicker Adam Vinatieri converted a 48-yard field goal as time expired to give the Patriots a 20–17 win and their first ever league championship. When discussing the game winning drive, Madden stated that "what Tom Brady just did, gives me goosebumps". Brady was named Super Bowl MVP while throwing for 145 yards, one touchdown, and no interceptions. At the age of 24 years and six months, Brady became the youngest quarterback to win a Super Bowl, surpassing Joe Namath (III) and Joe Montana (XVI). Bledsoe was traded to the Buffalo Bills in April, which cemented Brady's status as the Patriots' starting quarterback in 2002.