Real Madrid rested many of their first team players.
The victory means Madrid have now defeated the Catalan giants twice within the space of one week.
The Spanish champions, earlier on Tuesday, defeated Barcelona 3-1 in the Copa del Rey, to progress to the final of the competition, 4-2, on aggregate after a 1-1 draw in the first leg.
An early goal by Karim Benzema in the first half of Saturday’s encounter was cancelled out by Lionel Messi’s equalizer.
A header by Sergio Ramos deep in the second half helped Madrid secure a double over their bitter rivals.
Ozil, Higuain, Di Maria, Alonso, Khedira, Arbeloa, and Ronaldo, who all starred in Tuesday’s game, did not start on Saturday with the latter three coming on in the second half.
The players were rested by the Madrid coach for the second leg of their Champions League match against English giants, Manchester United, on Tuesday.
The first leg ended 1-1 at the Santiago Bernabau.
Despite Saturday’s victory, Madrid are still 13 points behind Barcelona in the Spanish League.