For the 2009 season, Yankees manager Joe Girardi switched Jeter and Damon in the batting order, with Damon moving to second and Jeter to the leadoff role. Jeter batted .334, third-best in the AL, with a .406 OBP, an .871 OPS, 18 home runs, 66 RBIs, 30 stolen bases in 35 attempts, 107 runs scored, 72 walks, and 212 hits (second in MLB). Defensively, Jeter committed a career-low eight errors, and his .986 fielding percentage was his career best. The addition of Gold Glove-winning first baseman Mark Teixeira allowed second baseman Robinson Canó to shift his focus to his right, helping Jeter. During the season, the Sporting News named Jeter eighth on their list of the 50 greatest current players in baseball.
Jeter achieved two career hit milestones in the second half of the 2009 season. On August 16, 2009, against the Seattle Mariners, Jeter doubled down the right-field line for his 2,675th hit as a shortstop, breaking Luis Aparicio's previous major league record. Then, Jeter became the all-time hits leader as a member of the Yankees (2,722), passing Lou Gehrig on September 11, 2009. The hit was a single off Baltimore Orioles pitcher Chris Tillman in the third inning.
In the 2009 postseason, Jeter batted .355, including .407 in the 2009 World Series, as he won his fifth World Series championship. He was named Sportsman of the Year for 2009 by Sports Illustrated, and won the Roberto Clemente Award, Hank Aaron Award, his fourth Gold Glove Award and his fourth Silver Slugger Award. Jeter also finished third in the AL MVP voting, behind Minnesota's Joe Mauer and Yankee teammate Mark Teixeira. It was also the fifth championship for Pettitte, Posada, and Rivera, who along with Jeter were referred to as the "Core Four".
In the 2009 World Baseball Classic, Jeter again started at shortstop. He was named captain of the United States team by manager Davey Johnson, and he batted 8-for-29 (.276) in eight games. Jeter and the United States team faced the Yankees at Steinbrenner Field in an exhibition game, the only time Jeter played against the Yankees.
Since 2009, Jeter has served as an ambassador for Weplay, a website designed to encourage children to get involved in sports. Jeter, along with Japanese baseball player Hideki Matsui, took part in a charity baseball game at Tokyo Dome to raise funds for survivors of the 2011 Tōhoku earthquake and tsunami.