The team announced the move Monday in a press release. Duncan, who retired in 2016, is the Spurs' all-time leader in points, rebounds and blocks, and was the only player to be on all five of the franchise's NBA championship teams.
"It is only fitting, that after I served loyally for 19 years as Tim Duncan's assistant, that he returns the favor," Popovich said in a statement.
Duncan played 19 seasons with San Antonio and won five NBA titles, earning three NBA Finals MVP awards. He was a 15-time All-Star and was named the NBA's Most Valuable Player twice (2002-03) in his career.
The Spurs also announced that Will Hardy, who started in the video room with the team, will take on an expanded role as an assistant coach under Popovich.
Hardy originally joined San Antonio in 2010 as a basketball operations intern after graduating from Williams College.
"Will Hardy is a talented, young basketball mind who has earned a great deal of respect from everyone in the organization thanks to his knowledge, spirit and personality," Popovich said in a statement.
Duncan and Hardy replace former assistant coaches Ettore Messina and Ime Udoka, who left the team this off-season. Udoka joined the Philadelphia 76ers as an assistant in June, and Messina jumped overseas to serve as head coach of the LBA's Olimpia Milano.
Becky Hammon and Chip Engelland are returning as Spurs assistant coaches for the upcoming season.