Al Shabab defender Hassan Maaz put through his own net after 33 minutes to hand the home side the points and completed a miserable night by getting himself sent off six minutes from time.
With the victory, the Hazfi Cup champions topped Group D on 13 points, three ahead of the visiting Saudi Arabians who needed a win in Iran to make the knockout stages for the second consecutive year.
Despite a point being enough for them to advance, Sepahan showed their attacking intentions early and dominated the opening exchanges.
However, the first chance of the game fell to Al Shabab completely against the run of the play after quarter of an hour but Ahmed Ateef fired over the bar, while Abdoh Autef’s neat pass was just beyond striker Naji Majrashi.
But Sepahan broke the deadlock just after the half-hour mark in fortuitous fashion when Mohsen Bengar’s long throw into the box was turned into his own net by Maaz as the defender attempted to clear the ball under pressure from Seyed Mohamad Salehi.
Maaz almost turned from villain to hero three minutes later but his powerful right-foot drive was pushed behind by Sepahan goalkeeper Mohammad Savari.
Iraqi striker Emad Mohammed then threatened for the home side as he ghosted past Al Shabab defender Saleh Sadeeq before curling an effort towards the far corner which keeper Mohammad Khojah clawed away at full stretch.
Maaz then saw his 40-yard free kick held by Savari as the visitors were unable to get back on terms before half-time.
Sepahan stepped up the pressure on Al Shabab after the break and created several scoring chances but could not increase their lead.
The home side came close to doubling their advantage after 53 minutes when Emad Mohammed rounded Al Shabab Khojah and rolled the ball towards an empty net but defender Abdulmohsen Al Dosari got back to clear off the line.
Mohammed saw another effort well saved by Khojah on 76 minutes before Al Shabab’s Nashat Akram fired wide when well placed after good work from Fisal bin Sultan.
However, Haaz was dismissed after 84 minutes when he stamped on Mohammad Nori’s back and Japanese referee Yuichi Nishimura had no option but to produce a red card.
Bin Sultan nearly scored a late equaliser for the 10-man Saudi’s but his strike from the edge of the area was cleared off the line by Mohsen Bengar.
