After a goalless first half it was the visitors who went ahead when Ibrahima Toure headed home in 51st minute before Sepahan added a second just nine minutes later when Al Hilal keeper Abdullah Alsdairy managed to turn Fabio Januario’s corner into his own net.
It seemed Sepahan were coasting to victory but Christian Wilhelmsson struck in stoppage time to ensure a nervy few minutes for Farhad Kazemi’s side.
The win means Sepahan move top of Group A with three points, two ahead of Al Jazira and Al Gharafa who played out a goalless draw in Abu Dhabi.
Chances were at a premium through much of the early stages of the first half and Wilhelmsson summed up the quality of the few opportunities that were created when his speculative 25th minute effort ballooned off a defender and was comfortably held by keeper Mahdi Rahmati.
The first real opportunity arrived in the 34th minute when a long ball was played into the area and Nawaf Alabid raced between two defenders and rose to meet the cross but could only direct his header at the Sepahan keeper.
But six minutes into the second half it was Sepahan who got their noses in front when a long throw bounced through the area and found Toure unmarked at the far post and the Senegalese striker directed a header against the edge of the woodwork and into the back of the net.
Al Hilal looked to offer a quick response and a fine move by Wilhelmsson deserved more as the Swedish winger danced his way past three defenders before drilling a well-struck effort that was too close to Rahmati.
But instead it was Sepahan who went further ahead just before the hour when a corner by Januario was diverted into his own net by Al Hilal keeper Alsdairy.
That goal pretty much wrapped up the points for the visitors but Al Hilal continued to try and press for a goal as Mohammad Salem Al Qarni just failed to get his foot to a Wilhelmsson cross when well-placed inside the area.
But it was Sepahan who came closest to scoring again 10 minutes before the end when Milorad Janjus swept a low shot from just inside the area that Alsdairy did well to get a hand to and push onto the post.
The visitors took their foot off the pedal after that, seemingly content with their margin of victory.
However, Al Hilal pulled one back through Wilhelmsson from the left of the area with a well-hit effort in stoppage time and though the hosts pressed after that, Sepahan held on for the win.