Portugal winger Otavio scored in the 17th minute to build on last week's 1-0 win before Ronaldo added a late second, and Al Nassr will next face Al Ain after Hernan Crespo's side saw off Uzbekistan's Nasaf Qarshi through Soufiane Rahimi's injury-time winner.
Following a scoreless first leg, the side from the United Arab Emirates came back from going a goal behind to Akmal Mozgovoy's close-range strike in the 51st minute to level through Kodjo Laba's acrobatic effort four minutes later.
The game looked to be heading for extra time when Rahimi capitalised on a poor attempt to punch clear by Nasaf goalkeeper Abduvohid Nematov to slot home the winner for the hosts two minutes into added time.
The 2003 champions will meet Al Nassr in the next round after Otavio headed their opener through the legs of goalkeeper Vladimir Stojkovic from Abdullah Al Khaibari's angled ball into the penalty area.
Ronaldo narrowly missed adding a second when his 37th-minute header clipped the post but the former Real Madrid forward did strike with four minutes remaining, slotting into an empty net after beating Stojkovic to a late punt forward.
Earlier in the day, Anderson Lopes' 122nd-minute penalty earned Yokohama F. Marinos a last-gasp 1-0 win over Bangkok United to seal a 3-2 victory that sets up a quarter-final meeting with China's Shandong Taishan for Harry Kewell's team.
South Korea's Ulsan Hyundai also confirmed their progress to the next round with a 2-1 victory over Japanese second-division side Ventforet Kofu to complete a 5-1 aggregate win.
Ulsan added to their 3-0 first-leg advantage in the 12th minute when Kim Ji-hyun scored with an instinctive finish from close range after Um Wong-san's shot had come back off the post.
Kazushi Mitsuhiro headed in an 88th-minute corner to level the scores on the night but Joo Min-Kyu netted four minutes into injury time to confirm Ulsan's quarter-final meeting with Jeonbuk Motors, who eliminated Pohang Steelers on Tuesday.
On Thursday, Saudi champions Al Ittihad will meet Navbahor Namangan from Uzbekistan in Jeddah following a scoreless draw in their first clash while Al Hilal take a 3-1 lead into their second leg against Iran's Sepahan in Riyadh.
