He replaced Gabriel Calderon in the popular football team.
The Argentine coach led Persepolis to top of the Iran Professional League (IPL) table, three points ahead of Sepahan.
Shah Khodro club has confirmed departure of Yayha Golmohammadi by mutual consent.
Shahr Khodro sits sixth in the table with six points adrift of top of the table.
Golmohammadi has become Persepolis coach for the second time. He was named as the Reds coach in 2012 and left the team after one year.
The 48-year-old coach won two Hazfi Cup titles with Zob Ahan and one Iran Super Cup as a coach.
As a player, he has claimed three Iranian league titles with Persepolis and one Hazfi Cup.