Injuries have been a major problem for the Sixers, who are already without No. 1 overall draft pick Ben Simmons, who sat out the entire season, and Joel Embiid, who played 31 games, because of injuries.
Okafor has been bothered by problems with his knee since undergoing surgery last year to repair a torn meniscus. Trouble with his knee arose again when he banged his knee on March 22 against Oklahoma City.
The team decided it is in his best interest to rest the knee the rest of the season.
Okafor, the No. 3 overall draft pick in 2015, averaged 11.8 points and 4.8 rebounds in 50 games this season. He averaged 17.5 points and 7.0 rebounds in 53 games as a rookie.
Covington has had soreness and swelling in his right knee, and an MRI performed Wednesday revealed a slight meniscus tear that may require surgery.
Covington played 67 games this season, all as a starter, and averaged 12.9 points and 6.5 rebounds.
The 76ers have already been eliminated from playoff contention.