Djeparov joined Esteghlal in 2017 on an 18-month contract but was loaned out to Sepahan for a six-month deal.
He returned to Esteghlal last season and spent a sensational season with the Blues and was selected as the best assist provider of the year.
Esteghlal will have a difficult task ahead in Iran Professional League and AFC Champions League since the team failed to sign an extension with Senegalese striker Mame Baba Thiam and Djeparov.
Djeparov has become the AFC Asian Footballer of the Year in 2008 and 2011.