Centre Lukhanyo Am (knee), flyhalf Handre Pollard (calf) and lock Lood de Jager (illness) are all missing from the group.
Their absence is a huge blow to the world champions after they played a pivotal role in helping the side lift the trophy in Japan four years ago and remain key players.
Am and Pollard have been placed on a standby list and could be integrated into the squad if injuries force others to withdraw in the weeks ahead.
"It's very sad, those are players who have done a lot for us and are players we need," Kolisi told reporters.
"They've won a lot of matches for us and they have experience. I don't have the words to sum up their contributions to the team.
"It has been tough to even talk to them. With Lukhanyo we found out (on Monday) that he wasn't going to make it. I spoke to him and he wasn't feeling very positive, you never know what to say.
"But with their injury timelines, there is hope that they might still come back into the team if anybody is injured."
Kolisi faces his own race against time to prove his fitness after a long-term knee injury means he has not featured for the Springboks this year but he has been named captain of the squad and could line up in warm-up games against Wales and New Zealand.
"I was scared, but the surgeon and the medical team at the Springboks gave me confidence that I would be okay," he said.
"It all reminds you how quickly it can all be taken away from you."
The Boks open their World Cup defence against Scotland in Marseille on September 10th and also have world number one side Ireland in their pool, with only two teams advancing to the quarter-finals.
