Barca returned to La Liga's summit – for at least a few hours – ahead of Real Madrid by defeating Diego Simeone's men in in the Spanish capital, though it was by no means straightforward.
Diego Godin had seemingly secured a point for the hosts with his header 20 minutes from time, but Lionel Messi popped up and scored a late winner for the second league match in succession to salvage what could potentially be a vital result in the title race.
Defeating Atletico also left Simeone's side seven points behind third-placed Sevilla and nine off Barca, as their chances of winning the league diminished even further.
"It was game against a direct rival," Luis Enrique told reporters. "It was of the utmost importance.
"Aside from actually getting the three points, it was important that we left Atletico further behind us.
"We changed our system to 3-4-3 to have more of the ball, more control. Atletico found it hard to keep up their pressing in second half, especially after a tough game midweek [in the Champions League against Bayer Leverkusen].
"Then our decisive players made difference."