Three-time NBA Most Valuable Player Jokic added eight rebounds, 13 assists, and three blocked shots for Denver, who won their eighth straight game and inched closer to the Los Angeles Lakers for the third seed in the Western Conference.
Jokic became the first center in NBA history with 40+ points and 10+ assists in a game without committing a single turnover.
MVP candidate Wembanyama, back after missing one game to rest a sore ankle, scored 34 points with 18 rebounds, seven assists, and five blocked shots for the Spurs, who led most of the contest but couldn't resist the Nuggets' late surge.
Aaron Gordon, fed by Jokic, threw down a dunk to tie it at 124-124 with 6.2 seconds left in regulation.
Wembanyama's jumper as time expired clanged off the rim and they went to overtime, when Gordon's dunk in the opening minutes put Denver ahead for good.
"It was indicative of what we can be as a group," said Gordon, who finished with 15 points.
Johnson scored 17 points, Jamal Murray scored 15 points and handed out 10 assists for the Nuggets in a contest marked by playoff-level intensity.
"We like the intensity," Gordon said. "That's a really good ball club over there that plays really hard. So they brought it out of us."
Two weeks before the start of the playoffs, Gordon said the victory over the West's second-placed team was an important marker.
"It's big," he said. "I just want us to be ready when the time comes. This was a good step in that direction."
Denver's Johnson drilled a three-pointer to open the contest, but Devin Vassell quickly tied it, and the Spurs didn't trail again on the way to a 72-65 halftime lead.
Things got testy late in the first quarter, when Wembanyama inadvertently caught Jokic in the face with his hand, and no foul was called.
However, angry Nuggets coach David Adelman and forward Aaron Gordon both received technical fouls and they were also called for a clear-path foul, leaving the Spurs to shoot three free throws despite Jokic being the one who was fouled.
Denver cut the deficit to one on Jokic's layup early in the third quarter and trailed by four going into the fourth.
San Antonio pushed their lead to 11 on a Wembanyama dunk with 9:08 left in regulation, Denver battling back to briefly take a one-point lead before they finished regulation all-square.
Around the league
The Detroit Pistons clinched the Eastern Conference top seed with a 116-93 victory over the Philadelphia 76ers.
Tobias Harris scored 19 points, and Jalen Duren and Daniss Jenkins added 16 points apiece to help Detroit capture the top seed, and home court advantage throughout the East playoffs, for the first time since 2007.
Jenkins added 14 assists for the Pistons, who improved to 8-2 since star guard Cade Cunningham was sidelined by a collapsed lung.
"The way this group has grown together as quickly as it has, it is special," coach J.B. Bickerstaff said. "But we've got more food to eat. We'll take tonight, enjoy this, but tomorrow we'll get back to work."
With center Joel Embiid sitting out the second night of a back-to-back, Tyrese Maxey scored 23 points to lead the Sixers, who slipped behind the Toronto Raptors for sixth place and the last direct entry to the playoffs.
Elsewhere, the Miami Heat, 10th in the East and jockeying to improve their play-in position, beat the Washington Wizards 152-136.
Jaime Jaquez Jr. scored a game-high 32 points off the bench for Miami. Fellow reserve Kel'el Ware added 24 points, 19 rebounds, and eight blocked shots and seven Heat players scored in double figures.
That included Bam Adebayo, who was heavily guarded after scoring 83 in Miami's last game against Washington and finished with 14. Center Will Riley scored 31 points to lead eight Wizards players in double figures, but Washington never led after the opening quarter.
