Al Duhail nearly broke the deadlock just before the break through Nakajima who took Bassam Al Rawi’s cushioned header first-time from the edge of the box but could not find the back of the net.
Rui Faria’s men came out from the dressing room a different side, taking the game to their opponents and soon taking the lead.
Mehdi Benatia marked his AFC Champions League debut with a goal, heading home Murad Naji’s cross to open the scoring for Al Duhail in the 56th minute.
Top scorer Youssef El Arabi doubled the Qatari side’s lead in the 74th minute. The Moroccan latched onto a Nakajima through pass and rounded Esteghlal goalkeeper Mehdi Rahmati before slotting into an empty net to make it 2-0.
Substitute Ali Afif sealed victory with the third goal after a swift counter attack. The Qatari international midfielder embarked on a 50-yard jinking run and then exchanged a one-two with Nakajima that left him with a simple tap in in added time.
Al Duhail will travel to Saudi Arabia to face Al Hilal on Matchday Two, while Esteghlal will welcome Al Ain to Tehran next Tuesday.