The Catalan outfit came from behind to record all three points at the Vicente Calderon and move onto nine points for the season.
Enrique has said that he "enjoyed every minute" of his side's performance in Madrid, but has insisted that there is still a lot of work to do in the months ahead.
"Both teams wanted the win, no doubt. We played at a very high level from the start and were very consistent. That a team like Atletico made so few chances showed we were very focused," Enrique told reporters.
"We dominated the defensive and attacking aspects of the game and even turned it around when things seemed to be going against us. I enjoyed every minute of my team's performance.
"I'm very happy as it was important to earn three points against a direct rival, but a lot remains to be done."
Lionel Messi came off the bench to secure all the points for the Catalan side.