The three-judge panel found that Jaramillo has the right to the money after he was improperly fired by former Sheriff Michael Carona.
Jaramillo helped prosecutors investigate Carona, who is serving a 5 1/2 year jail sentence for witness tampering.
Jaramillo pleaded guilty to tax evasion and federal corruption charges in 2007.
County officials had argued he wasn't entitled to an administrative hearing before dismissal because he was charged with state and federal crimes.
The City News Service contributed to this report.