It was an uphill victory from the start for Serbia, who dug themselves out of a 24-point first half hole to reach the brink of a regulation victory only to watch Patty Mill hit a desperation fade away jumper with 1.4 seconds to play to force the extra session.
With just over a minute to go in overtime and Serbia trailing 90-89 Jokic came to his country's rescue, scoring two clutch baskets to deliver the dagger and a 93-90 lead.
Bogdan Bogdanovic made the final two free throws to seal the victory.
Jokic finished with a team high 21 points and 14 rebounds, while Bogdanovic contributed 17 points to the Serbian cause.
The win sends Serbia through to the semi-finals for the second in the last three Games, where they now await the winner of U.S. and Brazil.
"Just amazing," said Bogdanovic praising Jokic. "Defensively, too.
"People don't see that a lot, defensively, he's tough as well. But I know he can play even better than that," Bogdanovic added. "He makes the game easy. It's fun to play with him."
Earlier, Franz Wagner hit for 18 points as Germany overcame a sleepy start to ease past Greece 76-63 and secure their spot in a first ever Olympic final four.
After group play in Lille, the basketball tournament has moved to Paris for the knockout round with four quarter-finals highlighted by a showdown between medal contenders France and Canada followed by the LeBron James-led U.S. taking on Brazil.
