Eller, 63, pleaded guilty to making false statements in a matter within a political subdivision, tampering with evidence, hindering apprehension or punishment of a criminal and violation of oath by a public official or officer.
The two deputies, Jessie Gibson, 56, and Chief Deputy Eddie Osborn, 41, faced aggravated assault and obstruction charges in connection with a July 9 shooting at the home of Gary Dean of Hiawassee. Dean, who was not injured, was "involved in an ongoing intimate relationship" with Osborn's wife, according to a Georgia Bureau of Investigation affidavit.
Gibson was found dead on Aug. 8 of a self-inflicted gunshot in what authorities called an apparent suicide.
Outside the courthouse Tuesday, Eller apologized to the residents of Towns County.
He wore an oxygen tube in his nose as he walked from the courtroom. Mike Weaver, his attorney, said Eller was suffering from diabetes and other health problems and could not answer other questions. He said Eller's sentencing is pending.