A second half goal from Omid Alishah in the 63rd minute proved to be the difference as Persepolis picked up their first three points in the group.
The two sides had met eight times in the competition, with Al Duhail just edging the head-to-head record with four wins to Persepolis’ three, while they only shared the spoils once in the 2017 Round of 16 encounter at Azadi Stadium.
Al Nassr also defeated Tajikistan’s Istiklol 3-1 in the group.
Al Duhail’s next match sees them travelling to Riyadh to face Al Nassr, while Persepolis welcome Istiklol to Tehran in Matchday 3.