Judge Neil Cohen says Quinn violated the state constitution by withholding the checks for two months because legislators hadn't addressed the state's pension crisis.
Lawyers were in Cook County court Friday, a day after a judge ordered Comptroller Judy Baar Topinka to immediately pay legislators the paychecks they've missed since the governor's July veto.
Lawmakers with direct deposit have already received paychecks, but 21 who only get paper checks haven't.
Legislators make a base salary of about $67,000, plus bonuses for serving in leadership. The bonuses haven't been paid either.
Quinn's attorneys say they're appealing and filing an emergency request to an state appeals court to stop the lawmakers from being paid.
The General Assembly reconvenes in late October. But there is no guarantee a pension reform bill will have been drafted by then. And if a bill is drafted, it has to be introduced and passed literally a few months before the primary election in March.
The governor was stung by more than his annual flu shot Friday.
"We're definitely going to appeal his decision to a higher court in Illinois," Quinn said. "I don't think anyone should get paid until we get pension reform."
The governor said he was not concerned about spending taxpayer money on the appeal.
"Every day, the taxpayers of Illinois pay $5 million more in liability on the pensions. That dwarfs any other cost," he said.
Committee member Republican State Rep. Darlene Senger said she is not convinced the benefit cuts on the table will save the state enough money.
"That savings number in my opinion isn't quite enough yet. And that's what we're still working on," Senger said.
No matter what the committee or courts do, the governor said he won't budge from his personal pension reform promise.
"I'm not going to take a paycheck until we get pension reform on my desk that we can sign into law," he said.
The belief is that Judge Cohen was trying to get money in lawmakers' hands as quickly as possible and to rule before the next lawmaker payday on Monday.
He wrote, "the governor's line item veto of house bill 214 violated Article IV, Section 11 of the Illinois constitution" that forbids the executive from reducing or eliminating legislator pay during a lawmakers' term.
Governor Quinn announced his veto in June, hoping to pressure 178 House and Senate members to pass reform legislation to address the state's $100 billion dollar unfunded pension liability.
"Illinois taxpayers can't afford an endless cycle of promises, excuses, delays and inertia," Quinn wrote.
State Senator Kwame Raoul applauded the judge's decision. Raoul chairs the House/Senate conference committee on pension reform and said the pay freeze had no effect on his panel's deliberations.
"If the judge had upheld the governor's action, any governor in the future on any issue however big or small could decide, 'Oh well I'm going to legislate, I'm going to veto legislators' pay,'" Raoul said.
Finally, there's the question of what will happen to Governor Quinn's paychecks. He voluntarily did not accept the July and August payments, and he has another check due Monday. He has not accepted them.
The Associated Press contributed to this report.