Real were already all but assured of a quarter-final berth after winning the first leg of their last-16 tie with Schalke 6-1 in Gelsenkirchen.
The Bernabeu hosts suffered a blow early on in when talented youngster Jese suffered what looked to be a serious injury.
His replacement, Gareth Bale, crossed from the right for Ronaldo to tap home and extend Real's advantage in the tie even further in the 22nd minute.
Tim Hoogland equalised for the Bundesliga outfit just after the half-hour mark, but two quick Real goals in the second half - Ronaldo netting his 41st of the season, and then Alvaro Morata getting on the scoresheet - ensured Carlo Ancelotti's side won the second leg as well.
Only four Madrid players who started the commanding victory in Germany were named in the starting XI for the return leg, with Iker Casillas, Sergio Ramos, Xabi Alonso and Ronaldo all keeping their places.
Jese was one of the fringe players brought in by Ancelotti but the 21-year-old's night was over almost immediately, the forward reportedly suffering a suspected anterior cruciate ligament injury in an innocuous tussle with Sead Kolasinac inside two minutes.
Bale did not need long to make a telling impact. With 22 minutes gone, good work by prolific Spain Under-21 striker Morata created the chance for the Wales star to work a yard of space on the right and drill in a low cross that Ronaldo turned home first time to take him past the 40-goal milestone for a fourth successive season.
Bale nearly had another assist five minutes later when he raced clear of his marker down the right and sent a perfectly-weighted pass into the area for Morata who had only make a telling connection to be sure of finding the net but instead fluffed his lines.
Despite their mauling three weeks ago, Schalke were a good match for Madrid throughout the half and deservedly pulled one back after half an hour when Hoogland was allowed to advance through the midfield before rifling an effort that took a massive deflection of Ramos to wrong-foot Casillas.
Isco's stinging 20-yard effort drew a good save from Ralf Fahrmann as Madrid sought an immediate response. Fahrmann then denied Morata, Ramos and Nacho as the hosts continued to press for another before the break, even with the overall leading standing at 7-2.
Yet it was the visitors who should have taken the lead on the night in the 40th minute. Madrid were sloppy in ceding the ball in midfield and Max Meyer was able to break away, the midfielder threading the ball through for Klaas Jan Huntelaar - who dragged his effort just wide of the post.
Fahrmann was back in action early in the second period when he somehow scooped Ronaldo's downward header over the bar, and again excelled in the 55th minute when he smothered Isco's shot after the midfielder had deftly cut inside his marker.
But Madrid's goal threat was ever-present and it came as no surprise when they regained the lead on the night with 74 minutes on the clock, Ronaldo collecting the ball in midfield and running powerfully at the back-pedalling home defence before drilling a low effort inside Fahrmann's near post.
Ronaldo could and should have been celebrating a hat-trick two minutes later when he fired against the bar with the goal at his mercy after Fahrmann had saved Morata's initial effort, but although Ronaldo had been thwarted the danger had not passed and Bale was able to steer the ball back towards the waiting Morata, who clinically slotted home.
There was still time for Ronaldo to wrap up his treble but when the opportunity came his way inside the final 10 minutes, his placed shot beyond the advancing Fahrmann came back off the right-hand post.