The 23-year-old Tsonga, who lost to Novak Djokovic in the Australian Open final, is still undergoing physical therapy following a knee operation, according to the French tennis federation.
"In agreement with Bernard Montalvan, doctor for the French team, Jo-Wilfried Tsonga believes he is not ready to participate in the games," the French federation said in a statement.
Tsonga will be replaced by Michael Llodra for the tennis tournament at the Beijing Games.
The 31-year-old Koubek has a back injury and will be replaced by Chris Guccione of Australia in the men's singles competition, with Mara Santangelo replacing her 21-year-old Italian teammate in the women's singles.
Knapp hasn't played since losing to Maria Sharapova in the third round of the French Open.