The 39-year-old's contributions moved Al Nassr nearer to the last eight, needing just three points from their final three group games.
Al Nassr captain Ronaldo had looked destined to endure a hugely frustrating game following a series of missed opportunities in the first half at Al Bayt Stadium.
However, the Portugal star finally opened the scoring little more than 50 seconds into the second half, when he headed home Sultan Al Ghannam's cross from close range.
Al Nassr then doubled their advantage through Angelo Gabriel, a summer signing from Chelsea, on 58 minutes, before the Brazilian turned provider six minutes later to tee up Ronaldo for his second.
The goal took the former Manchester United, Real Madrid and Juventus forward to four goals in this season's rebranded competition before he was replaced on 74 minutes.
Al Gharafa did pull one back through Joselu, a former team-mate of Ronaldo at Madrid.
Yet their hopes of an unlikely late rally disappeared when Seydou Sano was sent off six minutes from the end of normal time for a second bookable offence.
The win ensures Al Nassr remain unbeaten through five matches in the Western side of the draw, and move second in the 12-team table.
Super-sub Toney
The Riyadh club now sit behind only Saudi Arabian counterparts Al Ahli, who maintained their 100 percent record thanks to a double from substitute Ivan Toney to see off Asian champions Al Ain 2-1 in the UAE.
The England international was left on the bench for the match at Hazza Bin Zayed Stadium, however having been introduced on 65 minutes, he scored within five minutes. First, he headed home Riyad Mahrez's deep free-kick.
A late window signing from English Premier League club Brentford in August, Toney struck what proved to be winner four minutes later.
This time, he met a superb long pass from former Manchester City winger Mahrez to finish past Al Ain goalkeeper Khalid Essa.
Al Ain, who in April defeated Japan's Urawa Red Diamonds to win the title, pulled one back late on through Kaka's sublime volley.
The victory means Al Ahli have now won all five matches in the rebranded competition, and thus led the Western standings on 15 points.
Also in that section, Iran's Esteghlal were held to a goal-less draw by Uzbekistan side Pakhtakor Tashkent in Dubai.
