The vote means that the auditor and treasurer positions will continue to be decided by voters. Under the council-manager form, those positions would have been appointed by the county administrator.
With 80 of 89 precincts reporting, votes to keep the current form totaled 61 percent to 39 percent in favor of changing it.
Current auditor Cyrus Spradley and treasurer Linda Sharpe announced they would not seek re-election and that each is retiring effective June 30, 2013.
Charles Barton, an Aiken County Council member, easily defeated write-in candidate Daniel Turno for the auditor position with 97 percent of the vote.
Eleven write-in candidates were vying for the Aiken County treasurer position, but county registration and elections officials said the winner would not be determined until Wednesday because of the expected large number of write-in votes.