Los Blancos entered the match as the firm favourites to advance following a 6-1 victory when the pair met in the first leg of the last-16 clash last month.
The victory did not come without a price for Madrid, however, with youngster Jese Rodriguez leaving the field with a serious knee injury in the early stages of the contest.
Here, Sports Mole dissects the 90 minutes of action between the two European rivals.
On target: 14
On target: 5
Was the result fair?
With the outcome of the tie decided in the first leg last month, it had been feared that the fixture would be played at a pre-season pace. However, that was not the case. Both sides were inventive in the final third, but Madrid did not really hit top form until the latter stages of the second period, when they might have made the final score more comfortable. Schalke can certainly take credit for their performance on the night, but they had to rely on a number of fine saves from their goalkeeper Ralf Fahrmann. In truth, a 3-1 score at the Bernabeu was just about a fair reflection of the events on the field.
Los Blancos boss Carlo Ancelotti made a number of changes to his XI this evening with the Clasico in mind, but such is the strength of the Italian's squad, the home side were able to run out comfortable winners. Tonight was the perfect chance for a number of the fringe players to gain some valuable minutes, while Ronaldo and Gareth Bale were both in fine form ahead of the clash with Barcelona at the weekend. It was far from a vintage performance, with the team playing in second gear for much of the contest, but it was another composed and confident display from Madrid, who have now extended their unbeaten run to 31 matches in all competitions.
After conceding with 21 minutes on the clock, it would have been easy for Schalke to retreat into their shell and attempt to make the fixture purely a damage limitation exercise. However, the German outfit showed their character to respond and ultimately level through Hoogland, albeit via a deflection off Sergio Ramos. The visitors were certainly not short of chances throughout the 90 minutes and on another evening, might have secured a famous result at the Bernabeu. Julian Draxler and Klass-Jan Huntelaar were lively in forward areas, while Joel Matip was impressive in the back four. Overall, despite the defeat, a number of positives can be taken from their trip to the Spanish capital.
Sports Mole's man of the match
Cristiano Ronaldo: What more can be said about the Portuguese? The 29-year-old's two goals this evening took him onto 13 strikes in the Champions League this season, just one behind the total that Lionel Messi managed in the entire 2011/12 campaign. The attacker has scored 41 times for the capital outfit this season and registered 34 in his last 26 games in this particular competition. On another night, he might have had five or six, but he struck the woodwork twice, in addition to bringing a number of fine saves from the Schalke stopper.
Morata has found it difficult to command a regular spot for Madrid this season and despite impressing overall this evening, the Spanish Under-21 international struggled in front of goal. The 21-year-old had three or four clear opportunities, but his most glaring miss occurred in the first period when he fired wide after Bale had delivered a low cross from the right. The forward's relief was there for all to see when he found the back of the net late on, but the youngster should have scored three or four at the Bernabeu.
Overall, Sergey Karasev had a fairly comfortable night in Madrid. The Russian awarded just two yellow cards throughout the contest as both sides steered clear of late challenges. The home side might feel that they should have been awarded a penalty in the second period when Benedikt Howedes appeared to catch Morata inside the box, but the official was not interested. In truth, Karasev was not seen for long spells, which is always a good sign for a referee.
Madrid: It is the small matter of El Clasico at the weekend as Los Blancos welcome Barcelona in La Liga. As it stands, Madrid sit four points clear of the current champions at the top of the division.
Schalke: Schalke could move second in the Bundesliga table with victory against Eintracht Braunschweig on Saturday afternoon.