Jaber Ansari gave the visiting team a lead in the 8th minute, but Jalal Rafkhaei equalized the match with a header in the 17th minute.
Five minutes later, Mohsen Karimi scored for Esteghlal with a powerful shot from the edge of the area.
Later on, Malavan captain Pejman Nouri was brought down by Esteghlal goalkeeper Vahid Talebloo in the area and Rafkhaei converted his penalty.
Esteghlal stayed at the top of the table with 34 points, one point ahead of Esteghlal Khuzestan.
Elsewhere, Tractor Sazi Tabriz and Gostaresh Foolad shared the points, Siahjamegan defeated struggling Esteghlal Ahvaz 2-1, and Saba lost to Naft Tehran 3-1.