Nine-time French Open champion Rafael Nadal's loss in the quarter-final dropped him three places to number 10 in the ATP rankings, his lowest spot since April 2005.
The Spaniard has had a less-than-spectacular season by his standards, with just the one title on clay.
He was forced to miss the defence of his US Open crown last year due to injury.
1 Novak Djokovic
2 Roger Federer
3 Andy Murray
4 Stanislas Wawrinka
5 Kei Nishikori
6 Tomas Berdych
7 David Ferrer
8 Milos Raonic
9 Marin Cilic
10 Rafael Nadal
The Spaniard sustained the injury during practice in July and had been training with a cast on his right wrist, forcing him to miss the Rogers Cup in Toronto and Cincinnati Open.
Newly crowned Roland Garros champion Stan Wawrinka, who stunned world number one Novak Djokovic in the final, rose from number nine to four.
Wawrinka, who won his first grand slam in Australia last year, added a second major title to his name with the win in Paris.
Djokovic, who was unable to complete a career Grand Slam, maintained a healthy lead at number one.
The Serb has already secured his spot for the year-end championships in London, where he has triumphed the last three years.
It was Djokovic who beat Nadal at this year's Roland Garros, ending the Spaniard's 39-match winning streak at the event.
There was no change in the rankings for world number two Roger Federer and number three Andy Murray.
Sharapova loses two spots
Meanwhile, in the women's ranking, Maria Sharapova, who lost to Lucie Safarova in the fourth round of the French Open, fell from number two to four after failing to defend her title.
World number one and eventual champion Serena Williams' third French Open win and 20th Grand Slam title overall increased her lead at the top.
Safarova, the runner-up in Paris, moved from number 13 to a career-best seven after reaching her first Grand Slam final.
Swiss Timea Bacsinszky, who pushed an ailing Williams to three sets in the semi-finals, climbed nine spots to her best ranking of 15.
Women's rankings (top-10):
1 Serena Williams
2 Petra Kvitova
3 Simona Halep
4 Maria Sharapova
5 Caroline Wozniacki
6 Ana Ivanovic
7 Lucie Safarova
8 Ekaterina Makarova
9 Carla Suarez Navarro
10 Angelique Kerber
|Sharapova's failure to defend her French Open title cost her two spots in the rankings [Getty Images]
Source: Al Jazeera and agencies