The 34-year-old Swiss, initially seeded the third at this year's French Open, announced on Thursday through his Facebook account to pull out, admitting his fitness is "still not 100 percent", Xinhua reported.
It has been the first time for Federer, the 17-times Grand Slam champion, to miss from Roland Garros in 17 years, which has his running streak of 65 straight Grand Slam appearances snapped.
"It's definitely a loss for the tournament," commented Djokovic on Friday after the French Open main draw took place.
"We're not used to seeing Roger skipping Grand Slams, seeing that he hasn't missed one for 60-plus times.
"Obviously the nature of his injury is not light and it kept him off this tournament that I'm sure that if there was any chance he could play he would participate.
"But, you know, even without him the tournament is going to be played and I'm sure it's going to be an exciting one," added the Serbian.
Nine-times champion Nadal, who is promoted to the fourth seeding position with Federer's absence, told media that the former world No.1's withdraw was a blow to tennis fans.
"I think for me it's not changing much, but I understand that for the fans, for the tournament, for the world in tennis in general, it is a very negative news," said the fifth-ranked Spaniard.
Women's singles defending champion Serena Williams said it would be strange not to see Federer in Paris, but understood his worries.
"I think he plays most slams, so definitely -- 65 in a row? That's a lot. Whoo, cha! I don't know. I think it's just pretty awesome, but it means he cares about his future and the Olympics this year and Wimbledon and US Open," said the 21-times major winner.