Ginobili, who has missed 19 games since last playing on Feb. 11, has been out with a right ankle injury.
Popovich provided no explanation for Duncan's absence, but the move was not a surprise. The Spurs are coming off a home win over Golden State on Tuesday night, and Duncan already sat out back-to-back games earlier this month to rest his knees.
Duncan missed three games in late February with what was called a right quad injury.
Newly acquired forward Drew Gooden replaced Duncan in the starting lineup.