The convincing win saw Esteghlal finish second ahead of Iraq's Al Shorta on goal difference in Group A after both teams were level on five points.
Al Ahli had qualified for the knockouts earlier and ended up Group A winners with six points despite their defeat on Wednesday.
Teams in the group played only four matches each instead of the usual six after the UAE's Al Wahda were considered withdrawn from the tournament following several Covid-19 positive tests before they travelled to Qatar.
Esteghlal required a two-goal victory margin to make the cut and they did so with some flair on Wednesday as they dominated the game at the Al Janoub Stadium, one of the new venues in Qatar for the 2022 FIFA World Cup.
After a few missed chances, Mehdi Ghaedi put the Iranians ahead in the 29th minute with a powerful shot from the edge of the box following a pass from Farshid Esmaeli on the left flank.
Ghaedi, who was a constant source of menace for Al Ahli, was in the thick of the action once again in the 38th minute, but this time as provider.
The 57kg forward sent a perfect cross from the right flank for Mehdi Karimi, who got past his marker and headed home to make amends for an earlier miss when his shot had cannoned off the post after a great pass by Ghaedi.
Esteghlal didn't wait much after the break to increase their lead further with Malian forward Cheick Diabete heading home a chip from the edge of the box by Karimi in the 54th minute.
Al Ahli got their best chance late in the match but Esteghlal goalkeeper Sayed Hosain foiled a powerful 30-yarder from substitute Husain al-Mogahwi.