Sadio Mane had put Al-Nassr in front just before half time, with Ronaldo making it 2-0 in the 76th minute with a clever finish.
Although Al-Rayyan got a goal back through Roger Guedes late on, Al-Nassr still managed to prevail.
Ronaldo has now scored seven goals in eight games for Al-Nassr in all competitions this season.
In a change from his usual celebration, Ronaldo pointed to the sky after he scored.
Cristiano Ronaldo produced an emotional celebration after scoring for Al-Nassr
Ronaldo dedicated his goal to his father after scoring on what would have been his 71st birthday.
His father Jose died aged 52 of in 2005 of an alcohol-related liver condition when Ronaldo was 20 years old.
Ronaldo achieved a unique feat by scoring against Al-Rayyan.
As reported by Will Jeanes, Ronaldo has now scored more goals in his 30s than he did in his 20s.
Ronaldo has scored 441 goals in 523 games in his 30s, compared to 440 goals in 596 games in his 20s.
The Portuguese star recently reached the landmark of 900 career goals, with his current tally now standing at 904.