It was Sheen who demanded the child custody hearing following published reports that Mueller, 33, had checked into a rehab facility.
Both Sheen and Mueller were in court to attend the closed custody hearing in downtown Los Angeles. Los Angeles Superior Court Judge Hank Goldberg sealed the hearing at the request of Mueller's attorney, saying it was "in the best interest of the children" because of "questions of abuse and other inflammatory and emotional issues."
Sheen left the courthouse flanked by security and was on his way to catch a plane to Washington, D.C. for a performance of his stage show.
Mueller emerged from court smiling and hugged her attorney but declined to comment.
The proceeding lasted an hour, and attorneys for both Sheen and Mueller refused to comment after the hearing.
Mueller filed a restraining order against Sheen last month that temporarily stripped the actor of his custody rights. The couple's twins, Bob and Max, were removed from Sheen's home.
In filing the order, Mueller said that she was concerned Sheen was mentally unstable and that he had threatened her life with a pen knife in 2009.
The couple then reached an agreement, and Mueller dropped her request for a restraining order, but the ordeal kept Sheen from communicating with his sons.
Sheen and Mueller's divorce will be official May 2.
There are still two weeks remaining on Sheen's national comedy tour titled "My Violent Torpedo of Truth - Defeat is Not an Option."
Meantime, a Santa Monica judge considering Sheen's lawsuit over his firing from "Two and a Half Men" took no action Tuesday on the 45-year-old actor's request that the case be handled in a public courtroom.
Sheen sued Warner Bros. and "Two and a Half Men" executive producer Chuck Lorre for $100 million after his dismissal. He's suing for unpaid wages for the whole cast and crew. The actor claims he was sober and ready to work, but Warner Bros. and Lorre made him their scapegoat.
Warner Bros. fired Sheen last month after he went on a public rant against Lorre. Lorre's attorney calls the accusations "simply imaginary."
A judge heard two and a half hours of testimony Tuesday, but made no ruling in the case.