Atletico have yet to be beaten by Real in three meetings already this campaign after suffering a heartbreaking Champions League final defeat to Los Blancos back in May as they also won the Spanish Super Cup last month 2-1 on aggregate.
A second consecutive La Liga defeat for Real leaves Ancelotti's men six points adrift of Barcelona and four behind Atletico after just three games of the new league season.
And the Italian was at a loss to explain how his side petered out in the second period after a promising opening 45 minutes, just as they did in losing 4-2 to Real Sociedad a fortnight ago.
"The first half was good like at Anoeta and the second half wasn't," said Ancelotti.
"We played with intensity and aggression in the first half but failed to continue the momentum."
Real's deficiencies from set-pieces were once again laid bare after just 10 minutes as Tiago headed home Koke's corner.
However, the hosts responded through Cristiano Ronaldo's equaliser from the penalty spot and were only denied a half-time lead by some superb goalkeeping from Miguel Angel Moya.
It was a different story after the break, though, as Atletico grew into the game after the introduction of Arda Turan and Antoine Griezmann and won it 13 minutes from time when Turan swept the ball into the far corner from the edge of the box.
Atletico boss Diego Simeone, meanwhile, said his side's victory was a massive morale boast for a squad that has been overhauled after their La Liga winning campaign last season.
"I think it is the first time we have won twice in a row in the league at the Bernabeu and that is very important for our fans and a new group of players," said Simeone, who watched the game from the stands as he continues to serve an eight-game touchline ban.
Enrique hails Messi’s capabilities
Barcelona coach Luis Enrique hailed four-time World Player of the Year Lionel Messi as capable of things impossible even on computer game PlayStation after he set up Neymar twice in his side's 2-0 win over Athletic Bilbao on Saturday.
"It is evident that he is best in the world in any attacking aspect," he said.
"This version of Messi helps us a lot because he is a game changer. He does things in training that you can't imagine, things I haven't even seen on the PlayStation.”
COMMENTS
Comments are moderated and generally will be posted if they are on-topic and not abusive.
For more information, please see our Comments FAQ