Barca earlier beat Getafe by the same score thanks to a Dani Alves screamer and Bojan Krkic strike that put them eight points clear before Mesut Ozil added to Benzema's 11th-minute effort to trim the gap back to five with nine games remaining
Barcelona have 78 points from 29 matches with Real on 73.
Benzema initially struggled to win over Real coach Jose Mourinho but has been in a purple patch of form in recent weeks after his promotion to replace injured first-choice striker Gonzalo Higuain.
The France international's neat chip over Atletico goalkeeper David de Gea to open the scoring at the Calderon was his eighth in five matches in all competitions.
Atletico piled the pressure on the visitors after falling behind and Real had Spain's World Cup-winning goalkeeper Iker Casillas to thank for a string of saves that denied Sergio Aguero and Jose Antonio Reyes.
German international Ozil doubled Real's lead when he stroked Marcelo's low cross high past De Gea from the edge of the penalty area in the 33rd minute.
Argentina forward Aguero finally beat Casillas with a low shot four minutes from time to set up a nervous finale for Real but the hosts were unable to make their late pressure count.
EUROPEAN BLOW
Europa League champions Atletico have not beaten Real since a 3-1 success at the Bernabeu in October 1999 and their latest defeat, which left them in eighth on 39 points, was a blow to their hopes of playing in Europe again next season.
"One day they have to beat us," Casillas said in a television interview. "Today they pressed hard and maybe the result was unjust.
"Benzema is on a run and we have to make the most of it. He has made a radical change and we are very happy," he added.
Brazilian right-back Alves scored one of the goals of the season to put Barca in the driving seat at the Nou Camp.
A headed clearance looped into his path in the 17th minute and he caught the falling ball perfectly on the half-volley to send it fizzing past Getafe keeper Jordi Codina from 25 metres.
Krkic added a second with a deflected shot five minutes after halftime before Manu del Moral netted a fine volley in the 88th minute for the mid-table visitors to set Barca's nerves jangling in the final moments.
"More than the great goal I prefer to focus on the work of the team and above all the victory," Alves said. "We got a very important win against a very well-organised team," he added in a television interview.
EMOTIONAL NOU CAMP
There was an emotional atmosphere at Barca's vast stadium as the local fans paid tribute before kick-off to defender Eric Abidal, who had an operation on a liver tumour on Thursday.
Players from both teams wore T-shirts with a message of support for the France international as they walked out on to the pitch and there was an ovation for Abidal in the 22n
