Majid Aliyari opened the scoring for the visiting team at the Shohada-ye Shahr-e Qods Stadium in the 56th minute.
Omid Latifi made it 2-0 in the 70th minute and Aliyari completed his brace with three minutes remaining.
The Esteghlal spectators left the Stadium early in protest against the poor performance of their team.
Esteghlal remain 11th in the 16-team table with eight points out of seven matches.
The Tehranian side known as the Blues have suffered three losses so far.
They parted ways with Javad Nekounam last month following poor results but have failed to find a new replacement for their hot seat.
KI
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