Al-Nassr were already guaranteed a place in the round of 16 so Ronaldo, who has five goals in his last three matches, was rested on Monday night.
Al-Sadd took the lead through Akram Afif, named the Asian player of the year in November, eight minutes after the break.
While former Liverpool star Sadio Mane and Anderson Talisca went close for Al-Nassr, an own goal from close range by Romain Saiss made it 1-1 with 10 minutes remaining.
However, Afif was brought down in the area and, in the ninth minute of added time, Algeria's Adam Ounas converted the penalty.
The win ensured 2011 champions Al-Sadd booked a place in the round of 16, moving into fourth in the 12-team group, a point behind Al-Nassr in third. The top eight from each of the two groups progress to the knockout stage.
The AFC Player of the Year with a rapid counter-attack for the opener 💨— #ACLElite | #ACLTwo (@TheAFCCL) #ACLElite | #NSRvSAD pic.twitter.com/ifeENGvOr7December 2, 2024
"It was a tough and close game," Al-Sadd coach Felix Sanchez said.
"We worked hard to stop Al-Nassr having the ball, and to win at their home stadium. The players showed their character."
Al-Ahli are first in the group after the Saudi Arabian side was held to a 2-2 draw by Esteghlal.
Ex-Brentford striker Ivan Toney scored both goals for the hosts in Jeddah. Raphael Silva opened the scoring for the Iranian team after 42 minutes but Toney made it 1-1 just before the break from the spot.
Mohammad Hossein Eslami restored Esteghlal's lead six minutes after the restart but Toney scored his second penalty four minutes from the end, a fourth goal in Asia for the England international in the space of a week.
Elsewhere, Persepolis of Iran beat Iraq's Al-Shorta 2-1, while Al-Wasl of the United Arab Emirates drew 1-1 with Qataris Al-Rayyan.
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