He has been less than impressed with Los Blancos's lack of intensity, but also believes his men did more than enough to merit wins at home, with their failure to be clinical in the final third proving to be their worst enemy.
Pedraza hit the Real Madrid woodwork for the second time in the 76th minute following a mistake from Varane, and a late goal or two appeared certain with both defences looking shaky in the second period.
"I am happy for (Ceballos)".
Ronaldo came close to sending Real Madrid 3-1 ahead early in the second period after collecting a brilliant pass from Carvajal, but the attacker sent his low effort just wide of the post.
Father and son will be reunited, albeit on opposite sides of the ball, when Madrid visits the Basque Country club.
But Ceballos put Madrid back in charge when he fired in a ball that goalkeeper Fernando Pacheco spilled when he collided with a teammate while defending a cross.
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However, he capped his league debut with a fine first-half brace, either side of Manu Garcia's goal.
Real Madrid's team showed four changes from the one that started against Real Betis on Wednesday night, with Marco Asensio, Lucas Vasquez, Nacho and Dani Ceballos replacing Luka Modric, Toni Kroos, Marcelo and Gareth Bale.
Ronaldo's afternoon ended with Pacheco tipping his angled strike around the post, but Madrid nonetheless held on for the three points.
Madrid reportedly paid Betis 16.5 million euros ($19.7 million) for the up-and-coming midfielder.
Ronaldo then swung a volley towards goal from a corner, but his effort flew just over Pacheco's crossbar.
They may be seven points off the pace, but coach Zinedine Zidane has urged his troops to remain calm, as Real Madrid look to mount a comeback following a series of poor performances at home this season.