On Tuesday, the 6th U.S. Circuit Court of Appeals in Cincinnati sided with the Ohio Republican Party and ordered Brunner to set up a system that provides names of newly registered voters whose driver's license numbers or Social Security numbers don't match records in other government databases.
The GOP contended the information for counties would help prevent fraud.
But Brunner told the Supreme Court, "If the 6th Circuit's decision is allowed to stand, an untold number of legitimate voters in Ohio will be forced to re-establish the bona fides of their vote before the county boards of elections, or they will stay home out of frustration or confusion."
Her appeal brief also argued that the Republicans' fears of voter fraud are unsubstantiated and "hardly warrant such monumental interference with the electoral process."
Brunner has said mismatches between records can be the product of simple spelling errors or other innocent discrepancies, and that federal law never intended for mismatches to be the only grounds for disqualifying voters.
At least 200,000 newly registered voters have mismatched data, according to an initial review by Brunner's office. About 666,000 Ohioans registered to vote since January, many before the Democratic presidential primary election between Sens. Barack Obama and Hillary Rodham Clinton in March.
Brunner's office said Wednesday that she would comply with the lower court's ruling.
Brunner has called the issue a veiled attempt at disenfranchising voters and said other checks exist to help determine eligibility.
She said Republicans are trying to inject confusion at the last minute. The state's database matching registration information against Bureau of Motor Vehicle and Social Security records has been up and running in previous elections, including the 2006 gubernatorial election when Republican Secretary of State Ken Blackwell was in office, she said.
Ohio Republicans issued a statement calling the situation a shameful mess. They criticized her for filing an appeal after first saying she would comply with the earlier court ruling. Brunner said she has already taken steps to comply with the order despite the appeal.
"This appeal is stunning in its attempt to defy the law and conceal the fraud in this election," said Ohio Republican Party Deputy Chairman Kevin DeWine.
In court filings, the GOP has not produced any specific evidence of voting fraud, only unsubstantiated reports that voters from other states had cast fraudulent ballots during early voting.
The party has requested registration information for all voters in the state who registered and immediately cast a ballot during a weeklong period from Sept. 30 through Oct. 6.