Thomas was injured on a 6-yard catch in the first quarter of the Broncos' season-opening 21-20 win over the Carolina Panthers last week. Thomas caught four passes for 48 yards in the game.
An MRI turned up nothing that rules out Thomas against the Colts.
"I know what the issue is. We all know what the issue is," Thomas told reporters Thursday. "But it's about taking your time and seeing if you're ready come Sunday.
"It's day by day. I ain't gonna be feeling great. But it's getting better every day. You pray about it, keep getting treatment, and hopefully by game day, you're ready to go and nothing freaky happens."
Thomas was held out of Monday's practice and was limited in practice Wednesday and Thursday.
"But we were specific about what we asked him to do running routes and stuff," Broncos coach Gary Kubiak said. "He ran really well, particular things that we do for him, we try to script him the right way so he gets those reps and not have him waste a lot of running in a lot of other areas. Just trying to be smart with him."