Djokovic had lost his two previous finals since his 99th title win nine months ago at the Paris Olympics at Roland Garros.
But now he will head back to the same venue for the French Open in fantastic spirits after winning a tough final on Saturday two days after his 38th birthday.
"I'm just grateful to clinch the 100 here," Djokovic said in an on-court interview, with his family watching on in the Swiss city where some of his relatives reside.
"I had to work for it, that is for sure."
Djokovic joins fellow greats Jimmy Connors, who has a record 109 titles, and Roger Federer, on 103, as the only men with a century of tournament wins in the Open era.
The three-time French Open champion heads back to Roland Garros looking to add to his 24 grand slam singles titles.
He is set for a first-round match on Monday against American Mackenzie McDonald.
The Serb clinched with an ace down the middle to complete a surge to victory after breaking Hurkacz's serve for the first time while trailing 4-3 in the deciding set.
Djokovic took that break-point chance with a forehand cross-court winner advancing to the net on Hurkacz's sliced half-volley.
"Hubert was probably closer to the victory the entire match than I was," Djokovic said. "I don't know how I broke his serve."
Djokovic is now the first man in the Open era to win a title in 20 different seasons, his 100th singles title coming nearly 19 years after the first in July 2006.
That also was on clay, at Amersfoort in the Netherlands, against Nicolas Massu — the Chilean who now coaches Hurkacz.
"It's really inspiring how you present yourself on the court, off the court. It's just really incredible what you have achieved," Hurkacz said to the winner in the on-court trophy presentations.
Since the Paris Olympics, he had lost finals at the Shanghai Masters to Jannik Sinner last year, and the Miami Masters to Jakub Mensik in March.
Djokovic got much more than the match practice he came to Geneva for. He had fallen to quick exits in April from the previous tournaments he entered in the European clay-court season, at Monte Carlo and Madrid.
He also got to spend time with his extended family in the Swiss lakeside city where he has an aunt, uncle and cousins. His wife and children joined him in Geneva to celebrate his birthday after cutting a day of school, Djokovic quipped.
