The Spaniard rued the enforced substitutions of several players, who will be in a race against time to be fit for the club's upcoming Champions League fixture
Mesut Ozil's double and Karim Benzema's strike secured the win at the Santiago Bernabeu, but it came at a cost with Marcelo and Luka Modric forced off.
And Karanka has admitted their possible absence for the Champions League semi-final clash with Borussia Dortmund has taken the gloss off the result.
"Injuries were the worst part of the game," the 39-year-old told reporters after the match. "Marcelo felt a sharp pinch, while Modric indicated he noticed a muscle issue.
"I do not think goalkeeper [Diego] Lopez has anything serious though. We'll make changes as soon as we evaluate Marcelo's condition, but the important thing was to win.
"[Cristiano] Ronaldo and Ozil played the full 90 minutes with no problem. For Ozil, playing the whole match was important. It was a good chance to gain confidence."
The Spanish champions opted to start with Castilla midfielder Casemiro, and Karanka was left impressed by what he saw from the Brazilian and fellow youngster Nacho.
"The boy did really well and gave everything tonight," he continued. "Casemiro is a player we know well, one who has played in Brazil's first division and is an Under-20 world champion.
"We want players of personality and experience. Nacho always delivers too, and has shone for Castilla as well."
Los Blancos consolidate second in the Liga with their latest win, sitting six points clear of local rivals Atletico Madrid, who have a game in hand.