The San Antonio Spurs finished with 58-24 records for both the 2000-2001 and 2001-2002 seasons but found themselves suffering playoff ousters in both seasons from the eventual NBA Champion Los Angeles Lakers.

Prior to the 2002-2003 season, the team revealed their new logo, dumping the "fiesta colors" which had become unpopular with fans. Entering the 2002-2003 season, the team knew it would be memorable for at least two reasons, as David Robinson announced that it would be his last in the NBA and the San Antonio Spurs would begin play at their new arena (approved in 1999 by County voters), the SBC Center (now the AT&T Center), named after telecommunications giant SBC, whose corporate headquarters are located in San Antonio. This version of the San Antonio Spurs was very different from the team that had won the title a few years earlier. The San Antonio Spurs had remade their team in an attempt to dethrone the three-time defending NBA Champion Los Angeles Lakers. Second-year French star Tony Parker was now the starting point guard for the San Antonio Spurs and the squad featured a variety of three-point shooters including Stephen Jackson, Danny Ferry, Bruce Bowen, Steve Kerr, Steve Smith and Argentina product Manu Ginobili. Mixing the inside presences of Duncan and Robinson with the newer outside threats, the San Antonio Spurs earned a 60-22 record. In the playoffs, the San Antonio Spurs defeated the Suns, Lakers and Dallas Mavericks en route to facing the New Jersey Nets in the NBA Finals. The series against the Nets marked the first time two former ABA teams would play each other for the NBA Championship. The San Antonio Spurs won the series 4-2, giving them their second NBA Championship in franchise history. Duncan was named both the NBA Regular Season and Finals MVP for the season.

In the 2003-2004 season, the San Antonio Spurs were knocked out of the playoffs by the Lakers in the Western Conference Semifinals. The Lakers rallied from a 0-2 hole in the series and won 4 straight. The series was defined by a controversial game-winning shot in Game 5 by Derek Fisher with 0:00.4 left in the game. After the stunning loss, the San Antonio Spurs traveled to Los Angeles for Game 6, where they lost the game and the series. The San Antonio Spurs spent the following offseason tweaking the team.

With the acquisition of guard Brent Barry from Seattle, and the later additions of center Nazr Mohammed from New York (acquired in a midseason trade of Malik Rose to the dismay of San Antonio Spurs fans), and veteran forward Glenn Robinson from free agency, alongside regulars Bruce Bowen, Robert Horry, Tony Parker, Manu Ginobili, and Tim Duncan, the San Antonio Spurs finished the 2004-2005 season ranked number two in the Western Conference with a 59-23 record, finishing with the best record in the Southwest Division. In the postseason the San Antonio Spurs defeated the Denver Nuggets 4-1, the Seattle Supersonics 4-2 and the Phoenix Suns 4-1 before advancing to the NBA Finals, where they won the NBA championship for a third time in seven years by defeating the Eastern Conference champion and defending NBA Champion Detroit Pistons 4-3 on June 23, 2005. Tim Duncan was named Finals MVP, becoming only the fourth player to win the MVP award three times (joining Magic Johnson, Shaquille O'Neal, and Michael Jordan). Also, Manu Ginobili established himself as a NBA star, earning local, national, and international fan praise (particularly in his home country of Argentina ) and a berth in that season's All-Star Game.

In the 2005-2006 season, the San Antonio Spurs broke their franchise record for wins in a season (63-19) and qualified for the playoffs for the ninth year in a row. (The San Antonio Spurs and Indiana Pacers currently share the NBA's longest active consecutive playoff appearance streak with nine in a row — see Active NBA playoff appearance streaks.) However, the defending-champion San Antonio Spurs were eliminated in the second round by the Dallas Mavericks in a 7-game semifinal series that, due to a quirk in the playoff ranking system, featured the two top teams in the conference.

During the 2006 off-season, the San Antonio Spurs traded Rasho Nesterovic to the Toronto Raptors for Matt Bonner, Eric Williams, and a second-round draft pick in the 2009 NBA Draft.