Williams remained away from the team Wednesday after missing a game for personal reasons.
In a statement Wednesday, Williams said his resignation is effective immediately, citing health reasons.
"It is with great regret that I tender my resignation as the Defensive Coordinator of the Chicago Bears Football Club effective immediately," the statement said. "I am taking a step back to take care of my health and my family. I appreciate the opportunity to work with the Chicago Bears, a storied NFL franchise with a rich history. The McCaskey family is first-class and second to none. I would also like to thank Coach Matt Eberflus and General Manager Ryan Poles for giving me the opportunity to come to Chicago. I would also like to thank President Kevin Warren, the coaches and players of which I value the relationships and camaraderie. I value the NFL shield and all that it stands for and after taking some time to address my health, I plan to come back and coach again."
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Coach Matt Eberflus would not say if the two have spoken.
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Williams, in his second season as Chicago's defensive coordinator, missed last week's game at Tampa Bay after working the opener against the Green Bay Packers.
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Eberflus, a former defensive coordinator with Indianapolis, called plays against the Buccaneers and plans to do so "at this time" when the Bears (0-2) visit Patrick Mahomes and the Kansas City Chiefs on Sunday.
Eberflus said the Bears can get by without a defensive coordinator and doesn't see it becoming problematic because of the experience of his staff.
"I think with the experience that we have on defense, I don't think that's an issue," he said.
The Associated Press contributed to this report.