U.S. District Judge Barbara Crabb dismissed the district attorneys in Eau Claire and Milwaukee counties, a move the ACLU did not oppose.
Crabb says the case should be limited to public officials who are blocking the plaintiffs' access to marriage.
Eight same-gender couples filed the lawsuit in February, arguing the marriage ban denies them the civil rights that married couples enjoy.
The State Journal says Crabb also dismissed state revenue Secretary Rick Chandler because the plaintiffs have failed to show that he has any authority to decide whether same-sex couples can marry or receive tax benefits of married couples.
Gov. Scott Walker and Attorney General J.B. Van Hollen are among defendants remaining in the case.