Marco Belinelli's baseline jumper with 2.1 seconds left capped the Spurs' 95-93 victory at Indiana.
Popovich became the ninth coach with 1,000 regular-season wins and became the third-fastest to achieve the feat. He also joined former Utah Coach Jerry Sloan as the only coaches in league history to win 1,000 games with one team.
Tony Parker led the Spurs with 19 points, and Tim Duncan had 15.
Rodney Stuckey scored 18 for Indiana, which had its season-best winning streak end at three.
The Pacers appeared to take control by building a 79-65 lead after three quarters.
But the Spurs scored nine straight to tie the score at 91, tied it again at 93, took the lead on Belinelli's shot and held on when George Hill's three-pointer bounced off the rim.
San Antonio failed to give Popovich his grand party Sunday night when it lost at Toronto. The defending NBA champs weren't about to let that happen again, even when they were down 91-82 with 5:36 to go.
And, of course, the Spurs rallied by using Popovich's plan of getting everyone involved.
Danny Green started the rally with a layup. Kawhi Leonard completed a 3-point play. Duncan scored on another layup and when Parker knocked down two free throws with 3:18 left, the score was suddenly tied at 91.
Indiana answered with a 20-footer from Stuckey to retake the lead, but Aron Baynes tied it again with a tip-in with 56.7 seconds left to set up the final sequence — Belinelli's shot just before the shot clock expired and Hill's miss from the top of the key.
at Washington 96, Orlando 80: John Wall fell one point shy of his first triple-double of the season, Marcin Gortat had 14 points and 14 rebounds, and the Wizards beat the Magic to sweep the season series. Presented by Wizards owner Ted Leonsis with an NBA All-Star jersey before the opening tip, Wall hit a three-pointer a little more than a minute into the third quarter — the first shot made from beyond the arc by either team — to open an 11-0 run that put Washington in control. Wall wound up with nine points, 10 assists and 10 rebounds after missing a floater with about 50 seconds left. The Wizards have won two in a row following a five-game losing streak.
Golden State 89, at Philadelphia 84: Stephen Curry scored 20 points, Leandro Barbosa had 16 off the bench and the Warriors snapped the 76ers' four-game home winning streak. Klay Thompson and former 76er Andre Iguodala added 13 points apiece for the Warriors (41-9), who have won four of five and two straight after opening their four-game trip with a loss to the Hawks on Friday. Robert Covington scored 21 points to pace the 76ers (12-41), who committed 27 turnovers and shot seven for 24 from three-point range. Luc Mbah a Moute had 13 points and nine rebounds. The Warriors, the NBA's second-best three-point shooting team, shot just seven for 29 from behind the arc.
at Miami 109, New York 95: Chris Bosh scored 32 points, Mario Chalmers added 18, and Luol Deng and Norris Cole each scored 12 for Miami, which posted its biggest comeback win of the season after being down 14 early. Carmelo Anthony scored 26 points for the Knicks, who became the first NBA team this season to be guaranteed of finishing with a sub-.500 record. Anthony left in the fourth quarter to get his knee re-taped, but never returned. Amare Stoudemire scored 14 for New York. The Heat outscored New York 32-18 in the fourth.
at Milwaukee 103, Brooklyn 97: Khris Middleton scored 12 of his 18 points in the third quarter, and the Bucks rallied from a 17-point deficit to beat the Nets. Jared Dudley had 19 points for Milwaukee, which won its fifth straight home game. Giannis Antetokounmpo added 12 points and nine rebounds. After a poor-shooting first half, the Bucks turned up the defensive pressure and forced eight turnovers in a third quarter in which they outscored Brooklyn by 16. Jarrett Jack had 26 points for the Nets.
Atlanta 117, at Minnesota 105: Al Horford scored a season-high 28 points and grabbed eight rebounds, and DeMarre Carroll added a career-best 26 points. Paul Millsap had 19 points, nine rebounds and seven assists for the Hawks (43-10), who bounced back from a loss to Memphis the previous night. The NBA-leading Hawks still have not lost back-to-back games since Nov. 18. They shot 51% and outscored Minnesota 58-44 in the paint. Kevin Martin scored 21 points and Shabazz Muhammad had 18 points and eight rebounds in his first game since Jan. 9 because of a strained oblique for Minnesota. The Timberwolves lost for the first time in four games.
Utah 100, at New Orleans 96: Gordon Hayward scored 25 of his 32 points in the second half, and the Jazz overcame a 14-point, third-quarter deficit to beat the Pelicans. Derrick Favors scored 18 and Enes Kanter had 14 points and 11 rebounds for Utah, which won its second straight while handing the Pelicans their second straight loss. Eric Gordon tied a career high with seven three's on eight attempts and finished with 31 points for New Orleans, while Tyreke Evans added 18 points and 10 assists. But the Pelicans were unable to overcome the absence of leading scorer and rebounder Anthony Davis, who sprained his right shoulder on Saturday, and Ryan Anderson, who has a sore right elbow.
Oklahoma City 124, at Denver 113: Kevin Durant scored 40 points, Russell Westbrook had 26, and the Thunder handed the Nuggets their sixth loss in a row. Durant matched a career best by hitting seven three-pointers and finished 13 of 19 from the floor. Mitch McGary added 17 points and 10 rebounds for the Thunder. The Nuggets, who have lost 13 of 14, were led by Wilson Chandler's 23 points. Kenneth Faried and Ty Lawson each added 22 for Denver, which also lost its sixth straight at home — its longest home skid since dropping seven in a row in 2003.