The 29-year-old Serb started the tournament with $99,673,404 in the bank and the 294,000 euros ($328,303) he earned by beating Spain’s Roberto Bautista Agut took him past the landmark figure.
Top seed Djokovic defeated the Spanish 14th seed 3-6, 6-4, 6-1, 7-5 to move into a 28th consecutive Grand Slam quarter-final and 36th in all.
He will take on either Czech seventh seed Tomas Berdych or Spanish 11th seed David Ferrer for a place in the semi-finals.
Djokovic, seeking a first French Open title to complete a career Grand Slam, was 4-1 ahead of Bautista Agut in the third set when play was halted due to rain on Tuesday.
The Serb quickly wrapped up the next two games Wednesday and despite falling a break down to trail 2-4 in the fourth, he stormed back to claim victory on a second match point.
“With my coaching team, we had some tough talks on Tuesday night,” said Djokovic, who had struggled in the heavy conditions of the previous day when he had uncharacteristically dropped serve five times.
“But I came back today with more intensity even though it was a tough mental and physical battle.”
Roger Federer, who sat out Roland Garros through injury, has made $98,011,727 from prize money and stands second on the all-time list behind Djokovic.
LEADING PRIZE MONEY WINNERS:
Leading prize money winners in men’s tennis after Novak Djokovic passed the $100 million mark on Wednesday at the French Open:
Novak Djokovic (SRB) $100,000,875 (into QF at French Open)
Roger Federer (SUI) $98,011,727 (did not play French Open)
Rafael Nadal (ESP) $78,223,403 (lost 3rd French Open)
Andy Murray (GBR) $45,484,935 (into QF at French Open)
Pete Sampras (USA) $43,280,489 (retired)