Still smarting from the 3-0 reverse Wednesday in the second leg of the Copa del Rey semifinal, Real was unable to salvage pride in the La Liga clash and to make matters worse Barca has edged ahead in the all-time list of wins for matches between the two sides.
Barca has also gone 10 points clear of Atletico Madrid, which plays Sunday, and 12 clear of Real in what is turning into a one-team title race in Spain.
Victory completed the league double for Barca over Real, with a 5-1 thumping in the earlier fixture leading to the sacking of Los Blancos boss Julen Lopetegui after a sorry start to the current campaign.
Form has improved under Santiago Solari, but the only realistic chance of silverware for Real is another successful defense of the Champions League crown, languishing a distant third in the La Liga standings.
Both sides had chances before Ivan Rakitic put the visitor ahead in the 26th minute, playing a one-two with Sergi Roberto before lifting the ball over the onrushing Thibaut Courtois for a delightful opener.
It turned out to be the only goal of the game, an effort worthy of teammate Lionel Messi
and the Argentine maestro went close to adding a second, while Real's Ballon d'Or winner Luka Modric headed over from close range.
Real's frustration boiled over just before the break as captain Sergio Ramos appeared to deliberately elbow Messi, the two squaring up head-to-head with Barca players appealing to the referee to take firmer action against a player shown five previous red cards in El Clasico.
Ramos did go into the book in a second half in which his side was unable to put sustained pressure on Barcelona, which easily held on for its fourth consecutive league win in the Bernabeu.
It has also taken Barcelona ahead 96-95 in wins in the all-time El Clasico head-to-head as the balance of power shifts to the Catalans.
Missing the striking prowess of the departed Cristiano Ronaldo, Gareth Bale was substituted in the second half after an anonymous display, Karim Benzema and Raphael Varane went close towards the end but Real could not force an equalizer.
Solari praised his team's efforts, claiming it had been a "very equal" contest but it is Ernesto Valverde's Barca which is closing in on a fourth La Liga title in five years and with hopes of a treble still alive, in the final of the Copa del Rey and set for for the quarterfinals of the Champions League.