Chances remained few and far between in the second period, but a late Sergio Ramos header wrapped up all the points for Madrid.
Here, Sports Mole dissects the 90 minutes of action between the two La Liga rivals.
On target: 5
On target: 2
Was the result fair?
On the balance of play, Madrid certainly deserved to pick up all three points this afternoon. Barcelona, as expected, dominated the possession, but they managed just two attempts on target throughout the 90 minutes. The league title may have gone, but the capital outfit have shown that they are more than a match for Barcelona with back-to-back wins over the Catalan side.
Real Madrid's performance
With a number of their star players on the bench, Madrid struggled in the first period despite taking the lead through Benzema. Had Barcelona been at their stunning best, then the home side might have been in trouble. That all changed when Cristiano Ronaldo was introduced, however, with the Portuguese pulling his side to victory in the latter stages.
Barcelona are a stunning football team, that cannot be argued, but they are really struggling at the moment. They utterly dominated possession, as usual, but they struggled to create any real chances. It does appear that teams have just worked out how to quell the Catalan outfit - sit deep and absorb the pressure before breaking - with Madrid the best team in the world at doing just that.
Sports Mole's man of the match
Cristiano Ronaldo: With Madrid struggling in the second period, Mourinho sent for a certain Portuguese international. Ronaldo was just stunning in the latter stages as he outshone Messi once more, despite being on the pitch for just over 30 minutes.
Biggest gaffe of the match
With tempers running high after the final whistle, Barcelona goalkeeper Victor Valdes decided to get involved with the referee. His argument picked him up a red card, which just about summed up Barcelona's afternoon.
Miguel Perez had a productive 90 minutes of football this afternoon. It was not the most eventful El Clasico that has been played, although temperatures did rise in the second period. Barcelona thought that they should have been awarded a penalty late on, but the Spaniard quelled the calls.
Real Madrid: Mourinho's side are in Champions League last-16 action against Manchester United on Tuesday before travelling to Celta Vigo in the league next Sunday.
Barcelona: The Catalan outfit host Deportivo La Coruna in the league next Saturday before welcoming AC Milan in the Champions League on March 12.