"He was incredible tonight," said teammate Boris Diaw. "He really stepped up and made some incredible shots and brought a lot of energy."
Henderson said Mills is a tough player to cover.
"Not only is he a good shooter, he's a smart scorer and he can set the team up," Henderson said.
San Antonio came in having won its last three games against the Bobcats by an average of 28 points.
In this one, the Spurs never led by more than four points in the first three quarters.
The Bobcats jumped out an 18-6 lead behind Jefferson, who was active in the low post on both sides of the ball with 10 points and three steals in the first quarter.
Popovich countered by moving the more physical Diaw to bang in the low block with Jefferson instead of Duncan. Diaw turned out to be the best option, particularly with center Tiago Splitter sitting out with a calf contusion.
That helped slow Jefferson and the Bobcats. Jefferson was limited to four points the rest of the half with the Bobcats missing 22 of their last 31 shots before the break.
"He keeps (Jefferson) in front of him better," Popovich said of Diaw. "And he stays down on Al's pump fakes, which are maybe the best in the league. They're ridiculous."
Charlotte is clinging to the No. 8 seed in the Eastern Conference and aiming for its first playoff berth since 2010.
"We didn't play with level of discipline that we need to," Bobcats coach Steve Clifford said. "It was a good effort but we're going to have to play a much more disciplined game to beat a team like that."
NOTES: Along with Ginobili and Splitter, the Spurs were without Marco Belinelli (back spasms), Kawhi Leonard. ... Jefferson had scored at least 30 points in four of his last five games. Charlotte fell to 13-6 in games when Jefferson scores 22 points or more. They are 4-19 when he doesn't. ... Kidd-Gilchrist had a season-high 12 rebounds for the Bobcats. ... Mills' 18 points in the fourth quarter were the most in any quarter by a Spurs player this season.