Williams and defensive tackle Ryan McBean received six-game suspensions from the NFL and tight end Virgil Green will be suspended for four games.
The NFL said the players had violated the league's policy on performance enhancing substances.
"We are aware of this matter, but due to the confidentiality of the program, we are unable to provide additional comment on the situation," the Broncos said in a statement.
Williams recorded five sacks in 13 games during the 2011 season. McBean was credited with 33 tackles in 16 games, three of which he started.
Green, who was a rookie last season, caught only three passes for 24 yards. He played in all but one of Denver's regular-season games.
The players will be allowed to take part in off-season activities as well as exhibition games.