The Portuguese star, 39, was reportedly rested for the fixture in Riyadh given the Saudi club had secured their place in the knockout stages last week, with three rounds of the group phase remaining.
Ronaldo scored twice against Al Gharafa, another Qatari side, last time out, and then netted a double again in the Saudi Pro League on Friday.
However, the Al Nassr captain was omitted from Stefano Pioli's matchday squad for the visit of Al Sadd.
Ronaldo, who has 15 goals in 18 appearances for his club this season, was spotted at Al Awwal Park sitting alongside his mother Dolores Aveiro and his partner Georgina Rodriguez.
Al Sadd took the lead eight minutes into the second half through Akram Afif, when the reigning AFC Player of the Year raced from the halfway line onto a long ball.
Afif outpaced defender Mohammed Al Fatil and finishing low past Brazil goalkeeper Bento.
Al Nassr drew level on 80 minutes, once Brazilian youngster Wesley's low cross was turned into his own goal by Al Sadd defender Romain Saiss.
However, there would be a huge sting in the tail for Al Nassr, when Afif was tripped inside the hosts' penalty area and substitute Adam Ounas converted from the spot in the 99th minute.
With the defeat, Al Nassr stay third in the Western Region group stage, while Al Sadd move fourth to also claim a spot in the last 16.
The top eight teams qualify for the knockout stages.
Fellow Saudi side Al Ahli remain top - even if they surrendered their 100 percent record in this year's tournament – thanks to an Ivan Toney double that secured a 2-2 draw with Iran's Esteghlal in Jeddah.
The England striker twice equalised for the hosts from the penalty spot, with the first coming deep into first-half injury time and the second converted in the 86th minute. Esteghlal had Mohammed Hossein Eslami sent off five minutes before.
It represented a second successive Champions League Elite match in which Toney has scored twice following his double last week against Asian champions Al Ain.
