Zlatko Kranjcar's side dominated proceedings with first-half strikes from Bruno Cesar and Mohsen Bengar settling the contest as the Blues were clearly second best
The newly-crowned Iranian champions clinched their spot in the quarter-finals for the second consecutive season, while Esteghlal's poor recent record in continental competition continued.
Lively Albanian striker Xhehavir Sukaj played a key role in both goals, coming from Bruno Cesar and Mohsen Bengar as Sepahan dominated from start to finish, while the Blues disappointed in the highly anticipated affair.
After only three minutes, Sukaj brought out a good save from Blues keeper Mehdi Rahmati from an angled shot after a nice one-two with skipper Moharram Navidkia.
However only five minutes later the hosts went ahead when Navidkia's swerving effort from range was parried by Rahmati into Sukaj's path and he calmly headed centrally for Bruno Cesar to divert home with a deft touch.
On 22 minutes, Sukaj might have done better when he met Mehdi Jafarpour's right-wing cross but his header was straight at Rahmati.
Down the other end, Sepahan keeper Rahman Ahmadi was finally called into action on 26 minutes when Ferydoon Zandi whipped in a low cross which he dangerously fumbled but gathered at the second attempt.
In front of a strong home crowd, Sepahan eventually scored a second, when Fabio Januario's deep corner was headed back across goal by Sukaj, finding central defender Bengar who rose above Jlloyd Samuel to net his second goal in consecutive ACL games.
Esteghlal boss Parviz Mazloumi responded by throwing on French striker Goran Jerkovic before the break but the visitors continued to struggle to pose any threat.
The Blues did enjoy more attacking possession early in the second half, with Iran international Andranik Teymourian heavily involved, but they continued to fail to produce the final ball.
Sepahan had the better of the second-half opportunities, with Sukaj hitting the side netting, before Mehdi Karimian worked a one-two with Bruno Cesar only to fire over.
The second 45 petered out as Esteghlal's fate became clear with their desperation obvious when Mojtaba Jabbari fired a 40-metre strike high and wide on 74 minutes. Sepahan were content to hold their advantage to book their spot in the final eight of Asia's top club competition.