Gonzalo Higuain and substitute Karim Benzema also found the net as Jose Mourinho's side, chasing Real's first continental crown since 2002 and 10th European Cup, secured their place in Friday's draw for the last eight.
On a balmy night in the Spanish capital, Real took a deserved lead in the 26th minute when Sami Khedira sent Kaka clear on the left and the Brazilian crossed for Higuain to poke the ball into the net.
They doubled their advantage 10 minutes into the second half after goalkeeper Sergei Chepchugov could only divert Ronaldo's long-range strike on to a post and in and Benzema followed up his own shot to bag Real's third in the 70th minute, moments after coming off the bench.
Zoran Tosic rewarded the travelling CSKA fans with a goal 13 minutes from time when he rounded Pepe and lashed the ball high past Iker Casillas from just outside the area, prompting a furious reaction from Mourinho on the side of the pitch.
France striker Benzema, returning from a brief injury layoff, then unselfishly set up Ronaldo, who scored in the 1-1 draw in freezing Moscow in last month's first leg, to tap in his second and Real's fourth in stoppage-time.
It was the Portuguese international's 11th goal in his last seven appearances for Real and his 42nd of the campaign in all competitions.
"It wasn't spectacular but it was a mature display," Mourinho said at a news conference.
"Without doing anything out of this world we managed to dominate and the game was mostly played out in their half," the Portuguese added.
CSKA made a bright start to the game and should have taken the lead in the eighth minute when Seydou Doumbia sped clear but the Ivory Coast forward blasted a wild shot over the crossbar.
The home side gradually seized control and came close to a second shortly before half-time when Higuain just failed to get on the end of another low Kaka centre.
Chepchugov had to be alert to block a Ronaldo effort immediately after the break before Real midfielder Xabi Alonso picked up a booking that will keep him out of the first leg of the quarter-final.
CSKA occasionally looked dangerous on the break and tested Casillas several times with long-range efforts but never looked capable of producing an upset against the Spaniards, who are now unbeaten in the 18 Champions League matches they have played against foreign teams the past two seasons.
The only team to beat them in Europe's elite club competition during that period were their great local rivals and European champions Barcelona in last season's semi-finals.
"To obtain a result here we had to play our best game and make no mistakes," CSKA coach Leonid Slutski told a news conference.
"We contained them in the first half but we made mistakes and gave them the chance to attack us."
Real join Barca, AC Milan, APOEL Nicosia, Bayern Munich, Benfica, Chelsea and Olympique Marseille in Friday's draw.
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