John J. Cullerton, the president of the Senate, and Michael J. Madigan, the speaker of the House, sued Mr. Quinn, arguing that his action violated a section of the Illinois Constitution that says the salaries of members of the General Assembly cannot be changed in the middle of their term. In court last week, lawyers for the governor said that section of the Constitution should apply only to pay increases.

But in a decision released Thursday, Neil H. Cohen, an associate judge for the Circuit Court of Cook County, ruled against Mr. Quinn. He ordered Judy Baar Topinka, the state comptroller, who was also named in the lawsuit, to immediately pay lawmakers the money that was withheld, plus back interest. Ms. Topinka said in a statement that she had instructed her staff to begin processing the paychecks Thursday.

Mr. Cullerton praised the decision, saying it protected the separation of powers. “Now that the governor’s actions have been answered by a court, I trust that we can put aside all distractions and focus on the goal of pension reform,” he said, noting that a committee was making progress on a pension plan.

But Mr. Quinn said in a statement that he intended to challenge the ruling and would seek a court stay to prevent paychecks from going out until a higher court considers the case.