Real had gone ahead through a spectacular overhead kick from Sergio Ramos after 22 minutes but Ciro Immobile fired home minutes before halftime and a well-worked move was finished off by Ever Banega to put Sevilla ahead after 61 minutes.
Benitez's side raised their game but Fernando Llorente scored again with a header from a counter-attack after 75 minutes and substitute James Rodriguez's injury time goal was too little too late for Real, who suffered defeat at Sevilla just as Barcelona had last month.
"It is a difficult stadium to play in and I think we were a bit static against a strong side. You win leagues by going step by step and these are important points we have dropped," Ramos told reporters.
The in-form Brazilian Neymar, who now leads the La Liga scoring charts with 11 goals, opened the scoring for Barcelona with a clinical finish, having been set up by a defence-splitting pass from Sergio Busquets after 60 minutes.
Neymar and Luis Suarez have come to the fore in the absence of injured talisman Lionel Messi and Suarez converted a penalty after 70 minutes following a foul by Jaume Costa on Munir El Haddadi.
The two combined again, with Suarez finding Neymar who lifted the ball round Costa and knocked it home after 85 minutes.
The pair now have 16 goals between them from the last six games.
"We played well and created a lot of chances. We need to continue this way. I am happy with the way I am playing but I think I can still do better," Neymar told reporters.
An injury time header from Antoine Griezmann allowed third-placed Atletico Madrid to finally break down a defensive Sporting Gijon for a 1-0 victory.
Barca lead the table with 27 points from 11 games, three more than Real while Atletico are on 23 points.
Gareth Bale was fit to return to the Real attack after missing the previous four games while Rodriguez started on the bench, having returned to the squad after almost two months out through injury.
Defender Nacho Fernandez, who scored Real's only goal in their Champions League victory over Paris Saint Germain last Tuesday, hit the post with a swerving volley after 10 minutes.
Ramos showed his dexterity with an expertly taken overhead kick to give Real the lead but his problems with a shoulder injury were aggravated and he later had to go off.
Real missed his leadership at the back and poor defending allowed Immobile to score from a tight angle at a corner.
Sevilla carried the greater threat in the second half and Banega slid the ball home after good work from Yevhen Konoplyanka while Llorente headed home a Mariano Ferreira cross having been left unmarked in the area.
The home side were controlling the final stages of the game but Rodriguez still hit the back of the net with a fine 25 metre drive.
(Reporting by Tim Hanlon in Barcelona, editing by Clare Fallon, Pritha Sarkar and Ian Chadband)
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