Duncan joined Michael Jordan, Larry Bird, Magic Johnson, Bill Russell, Wilt Chamberlain, Kareem Abdul-Jabbar and Moses Malone as the only players to win the MVP award in consecutive seasons. Jordan had been the last to do so.
"Unbelievable," Duncan said. "I would never have imagined being even close to that list. Definitely an honor."
Duncan received 60 first-place votes and 962 points from a panel of 119 writers and broadcasters who cover the NBA. He edged Minnesota Timberwolves forward Kevin Garnett, who had 43 first-place votes and 871 points.
The 7-foot Duncan averaged 23.3 points and recorded career highs with 12.9 rebounds, 3.9 assists and 2.9 blocks per game in leading the Spurs to a league-best 60-22 record. He had 58 double-doubles and shot 51 percent from the field.
Duncan was named Western Conference Player of the Week five times. On Feb. 1, he registered a league season-high 25 rebounds. On March 14, he had 24 points, 15 rebounds and 10 assists for his second career triple-double.
Spurs Coach Gregg Popovich, who was named Coach of the Year on Monday, credited Duncan for playing a more assertive role with his teammates. He was especially integral in the development of point guard Tony Parker and rookie shooting guard Manu Ginobili.
Garnett led Minnesota to a 51-31 record, averaging 23.0 points, 13.4 rebounds and 6.0 assists. He paced the league with 68 triple-doubles and six triple-doubles and was MVP of the All-Star Game, scoring 37 points in leading the West to a double-overtime win.
"A lot of guys had great years this year and a lot of guys could have won this award," Duncan said.
Just 13 players received votes, with six receiving first-place votes. Los Angeles Lakers guard Kobe Bryant was a distant third with 496 points, followed by Orlando Magic guard Tracy McGrady (427) and Lakers center Shaquille O'Neal (126).
Last year, Duncan was chosen over New Jersey Nets point guard Jason Kidd, who received just 31 points this year.
Duncan, 27, has spent his entire six-year career with the Spurs and was MVP of the 1999 NBA Finals.
A five-time All-Star, Duncan has been named to the U.S. Olympic team in 2004. He was supposed to be on the 2000 Olympic team a year after winning the NBA title, but an injury forced him to withdraw.
San Antonio will play the three-time defending champion Lakers in the Western Conference semifinals. Los Angeles has knocked the Spurs out of the playoffs each of the last two years.
Voting was on a 10-7-5-3-1 basis.