"We are having a great year and we have to keep it going," said Atletico's Jorge "Koke" Resurreccion, who set up Diego Costa's goal. "Diego Costa is in a spectacular moment. He has helped us a lot."
Bale, Madrid's 100-million-euro man, went on at the start of the second half, finally playing in front of his new home fans after straining his left thigh while warming up before last weekend's match.
Yet neither the Wales winger in 45 minutes nor Cristiano Ronaldo in 90 were able to target Atletico's goal.
Atletico's last league win against Madrid had come in 1999, and since then it had gone 23 games without a victory.
But Atletico's victory over Madrid in the same Santiago Bernabeu Stadium last May to claim the Copa del Rey had apparently given it the boost in confidence it needed to break its horrendous streak.
While Atletico squeaked out that cup win in extra time, Diego Simeone's side simply outplayed Madrid on Saturday, creating many more shots and deploying a swarming defense that kept Madrid in check until the final minutes.
Simeone pumped both fists on the final whistle as he left the dugout, deservedly satisfied with his team's effort.
"We can play better or worse, but our commitment to working hard is non-negotiable," said Simeone. "The team is above all the rest."
Diego Costa, who also scored in last season's cup final, took the game's sole goal when Filipe Luis stole the ball from Madrid's Angel Di Maria and Koke placed a throughball for his goalscorer to coolly fire it in.
As the Brazilian forward soaked up the dismay of Madrid's supporters, Madrid coach Carlo Ancelotti turned away and slapped his leg in frustration.
"When things don't go well you have to reflect on the reasons," said Madrid defender Sergio Ramos. "They won the derby because we lacked the efficiency from recent years, but we can't live in the past."
Messi netted his goal in the 21st with a left-footed shot after combining with Pedro Rodriguez, but he asked to be replaced eight minutes later after hurting a muscle in his right leg.
Adriano sealed the result for Barcelona in the 56th from a pass by Cesc Fabregas while Messi watched from the bench.
Messi's injury leaves him in doubt for Tuesday's Champions League match at Celtic, when Atletico plays at Porto. Madrid hosts Copenhagen on Wednesday.
Barcelona said the Argentina forward would undergo more tests on Sunday.
While Barcelona may be missing Messi for the trip to Glasgow, it should have Neymar well rested after the striker didn't play a minute at Juegos Mediterraneos Stadium.
Barcelona's first-year coach Gerardo Martino has guided Barcelona to its best start in 82 leagues. Five other managers, including Pep Guardiola (2009-10) and predecessor Tito Vilanova (2012-13), had reached six wins.
"I have only latched on to one of the records that these players have broken and continue to break," said Martino. "They have been doing so for years both individually and as a team. The fact that I formed a part of this one is circumstantial."
Elsewhere, Jonas scored his third winning goal for Valencia this week to secure a 1-0 victory at home over Rayo Vallecano.
Jonas netted the decisive goal in recent wins against Sevilla and Granada, and he stepped up once again to produce the 36th-minute winner after intercepting a poor pass by Rayo's Saul Niguez.
Real Sociedad, meanwhile, was held to 1-1 at home by Sevilla before its Champions League game at Leverkusen on Wednesday.
