Luis Enrique's first Clasico in the Barca dugout got off to a dream start as Neymar continued a purple patch in front of goal to silence the Santiago Bernabeu crowd after four minutes.
Cristiano Ronaldo restored parity from the penalty spot before the break as Gerrard Pique was penalised for handball and the second half became a harrowing experience for the league leaders at times.
Pepe headed the hosts ahead in the 50th minute and Madrid should have boasted a heavier margin of victory, but they were unable to repeat the clinical 61st-minute finish provided by Karim Benzema on countless other destructive counter-attacks.
"The defeat makes it clear that they are as good as us or, as today, better," Luis Enrique told reporters.
"And we have to realise that. You can win or what happened today can happen.
"There wasn't much difference between us. We started well in the first half but once we scored we suffered.
"We could have made it 2-0 but it was a half of give and take. The second [half] asked more of us and we were punished.
"The opponent was better and the opponent deservedly beat us."
Barcelona retain a slender one-point advantage at the top of La Liga - Sevilla can go draw level at the summit with victory over Villarreal on Sunday - but Luis Enrique does not expect any long term scars from defeat to their bitterest rivals.
"I don't think we're deflated," he added. "We stopped creating chances because of our rival.
"The second goal is an attacking set-piece and they took advantage. The third goal was from our error. We were punished on the counter and it did us a lot of harm."