In the match held in Foolad Arena, Brazilian striker Luciano Pereira was on target twice in the 22nd and 32nd minutes.
Ayyoub Kalantari, who was sacked in the added time, pulled a goal back in the 90th minute from the penalty spot.
Foolad Khuzestan midfielder Sina Moridi was also shown a red card in the added time.
Raphael Messi Bouli made it 3-1 for Foolad in dying moments of the match.
Foolad moved up one place to sixth with 33 points, 18 points behind leader Persepolis.
Esteghlal Khuzestan sits bottom of the table with 10 points.
Also, Machine Sazi and Nassaji Mazandaran played out a goalless draw in Tabriz.
Machine Sazi and Nassaji are 9th and 10th in the IPL table with 27 and 26 points, respectively.