Jaramillo cooperated with federal authorities in the corruption trial of Carona, who was eventually convicted of witness tampering.
Judge Banks said the back pay will be calculated on the salary and benefits Jaramillo was making in March 2004, when he was fired, through January 28, 2007 -- the day before Jaramillo pleaded no contest to perjury and misusing public funds.
Jaramillo is scheduled to be sentenced on September 14.
The judge's final ruling on Jaramillo will be issued within three weeks.
Carona is to begin serving a five-and-a-half-year sentence on July 24.
City News Service contributed to this report.