The less-fancied visitors took an early lead as Diego Costa netted his eighth goal of the season following an exquisite through-ball from in-form midfielder Koke.
Costa was a nuisance throughout and was lucky not to receive a red card for squaring up to referee Mateu Lahoz, but Atletico left the door open for Real by not adding a second.
After a poor first half, Carlo Ancelotti threw on Gareth Bale for his home debut at half-time, but the world’s most expensive player was largely ineffectual.
Koke almost added a second late on as he hit a curling shot onto the crossbar, but there was still enough time for the hosts to waste two great chances.
Firstly, Bale saw his scissor-kick palmed away by Thibaut Courtois and then fellow substitute Alvaro Morata could only put his shot into the sidenetting as Atletico held on for a seventh consecutive league win.
That victory keeps Atletico in touch with Barcelona, who secured the club's greatest ever start to a league season by also winning against Almeria on Saturday.
Lionel Messi broke the deadlock in the 21st minute with a wonderful strike after cutting in from the right, but the Argentine had to leave the pitch with a thigh injury before the half-hour mark.
Barcelona’s disappointment briefly inspired Almeria, but the champions eventually doubled their lead in the second period when Adriano poked Cesc Fabregas’ low cross past Esteban in the hosts’ goal.
Elsewhere, Sevilla faced a tricky test at Anoeta against Real Sociedad at the end of a week that saw their winless run away from home in the league stretch to over 12 months.
Sevilla's last away success came against Deportivo La Coruna on September 24 of last year, but they got off to a great start at San Sebastian as Jairo Samperio slotted past Claudio Bravo following Ivan Rakitic’s exquisite lofted through-ball.
However, after Piotr Trochowski incredibly missed an open goal towards the end of the first half, Sociedad equalised through Antoine Griezmann in the second period.
Juan Cala received a red card late on for the visitors, but they held on for a commendable point.
Valencia’s recent resurgence continued in Saturday’s early kick-off against Rayo Vallecano, as they picked up their third consecutive La Liga win after a run of four defeats in all competitions.
Rayo came into the match on the back of five straight losses in the league and Valencia made sure that run would continue.
Jonas’ fourth goal in three games was enough for the home side to clinch three points in order to move into the top six.
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