Poor defending from two corner kicks proved to be the Uzbek's downfall as Ibrahima Toure opened the scoring after 73 minutes when the striker headed home from six yards after Hadi Aghily had nodded a deep set piece back across the face of goal.
Sepahan doubled their lead almost immediately afterwards when Mohsen Bengar was afforded all the time and space he needed to meet Ehsan Haji's corner with a powerful header at the back post that keeper Temur Juraev was unable to keep out.
The result was sweet revenge for the hosts following the 2-1 defeat to Pakhtakor in Tashkent last week as the Iranians closed to within a point of their opponents.
Sepahan had the first sight of goal after nine minutes when Toure curled a shot towards the far corner that Juraev comfortably held.
The only other highlight of a dour first-half saw Emad Mohammed blast wide on the half-hour mark when well-placed inside the box.
The second period began in more lively fashion as Mehdi Karimian was played in by Bengar but Juraev was equal to his right-foot effort.
Pakhtakor hit back shortly after and Artur Gevorkyan had a good chance to open the scoring but diverted a cross over the bar with just keeper Mehdi Rahmati to beat.
Ahmad Jamshidian called Juraev into action once again shortly after the hour mark when the midfielder controlled Haji's long pass but Juraev did well to get down low at his near post to save with his feet.
Sepahan then broke the deadlock in the 73rd minute thanks to some slack marking from the Pakhtakor defence as Aghily, under no pressure, was allowed to head a deep corner back across the six-yard box and Toure beat Bojan Miladinovic to the ball to nod his side in front.
Two minutes later, Sepahan doubled their lead from another set-piece as Haji's out-swinging corner from the left was met at the back post by two Sepahan players in acres of space, Bengar getting there first to power a header that Juraev was unable to prevent from crossing the line.
That proved to be the last meaningful action as Sepahan comfortably closed out their first victory of the 2010 AFC Champions League.