Last year's runners-up took the lead through Mohamed Reza Khalatbari in the 11th minute.
Jaralla Al Marri quickly equalised but Igor Castro (Igor Jose Marigo De Castro) made it 2-1 in the 24th minute and, after Itamar Da Silva was sent off, Ghasem Hadadifar sealed Zob Ahan's victory 19 minutes from the end.
Zob Ahan now have seven points from three games whereas their Qatari opponents, missing a number of players through injury, lie bottom of Group D with just one point.
Following a cagey opening, Al Rayyan skipper Fabio Cesar found national team colleague Al Marri but the latter shot straight into the hands of Zob Ahan goalkeeper Shahab Gordan.
Two minutes later, Zob Ahan's Mohammed Hoseini saw a powerful effort from close range blocked by Al Rayyan’s Korean defender Cho Yong-hyung.
However, the resultant corner yielded a freak opening goal as Khalatbari's kick caught the wind and was carried directly into the Al Rayyan net.
The lead did not last long, though, as Al Rayyan captain Cesar curled in a fierce free-kick which rebounded off the post for an unmarked Al Marri to pounce and hammer the loose ball past the helpless Gordan.
But another Khalatbari corner saw Zob Ahan retake the lead midway through the first period. His delivery was met by a weak punch from keeper Soud Abdulla and Igor Castro, unmarked five yards out, steered the ball into the top corner.
Abdulla was more secure five minutes later when he safely gathered Esmaeil Farhadi’s instinctive header to keep the deficit down to a single goal.
However, Al Rayyan suffered a further setback in the 59th minute when they went down to 10 men due to a sudden rush of blood by Itamar (Itamar Batista Da Sila), who in a fit of anger stamped on Farhadi.
Lebanese referee Andre El Haddad calmed fraying tempers on both sides before showing the red card to the Brazilian striker.
Gordan was then booked for time wasting but there was no further need for such tactics once Hadadifar made the game safe in the 71st minute.
With time to size up his options some 30 yards out, the midfielder opted to let fly with a powerful left-footed effort which whistled past Abdulla and into the roof of the net.