Senin Sebai scored on the break to put the club from Dushanbe in front with a minute left in the first half and Istiklol held out under relentless pressure until Ronaldo levelled with a clever clipped finish in the 66th minute.
Anderson Talisca headed the Saudi outfit in front six minutes later and the Brazilian put the result beyond doubt with 13 minutes remaining when he stroked a low shot into the corner.
The victory was Al Nassr's second in a row in the group stage of the competition and moves Luis Castro's side three points clear at the top of Group E.
Iran's Persepolis are in second place following a 1-0 win over Al-Duhail of Qatar, with Omid Alishah scoring in the 63rd minute to earn the 2018 and 2020 runners-up their first victory of the campaign.
Al Ittihad's meeting with Iran's Sepahan in Group C was called off as players from the Saudi club refused to leave their dressing room due to a statue of assassinated Iranian general Qasem Soleimani being placed at the entrance to the pitch.
The Asian Football Confederation said the game, which was due to be played in Isfahan's Naghsh-e Jahan Stadium, had been "cancelled due to unanticipated and unforeseen circumstances".
Also in Group C, Al Quwa Al Jawiya beat OKMK 2-1 after Ali Jasim scored his third goal in two Asian Champions League games to give the Iraqis a second-minute lead over the Uzbekistan team with Sanzhar Tursunov's own goal doubling the visitors' lead.
Siavash Haghnazari pulled one back for OKMK with nine minutes to go but Al Quwa Al Jawiya held on to win and reach four points, one ahead of Al Ittihad.
In Group B, Uzbekistan's Nasaf Qarshi climbed into pole position after claiming their second win in a row when Azizbek Amonov struck twice in a 3-1 win over Al-Sadd of Qatar.
Ruzikul Berdiev's team hold a two-point lead over Al Sharjah from the United Arab Emirates, who beat Jordan's Al-Faisaly Amman 1-0 thanks to a 20th-minute goal from Moussa Marega, an Asian Champions League winner with Saudi Arabia's Al Hilal in 2021.
The 10 group winners advance to the last 16 along with the three second-placed teams with the best records in the western and eastern halves of the competition.
