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.
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.
"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.
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.
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.
