Thomas, who suffered a setback earlier this month when he strained a groin while rehabbing from his initial injury, was limited in the 20 minutes of practice that were open to the media.
Thomas was hurt within five minutes of free agent nose tackle Ty Warren going down with a torn triceps during a drill during training camp. Warren underwent surgery and was placed on I.R. for the second straight season.
The Broncos (1-2) haven't had their top three defenders on the field at the same time this season, but cornerback Champ Bailey (hamstring), middle linebacker D.J. Williams (elbow) and pass-rusher Elvis Dumervil all practiced Wednesday.