Diego Simeone's side had seen city rivals Real clamber above them into first place by virtue of their head-to-head record after their Wednesday win at Cadiz.
Marcos Llorente proved instrumental in Atletico's win, setting up Angel Correa for the opening goal shortly before the break, and also providing for Yannick Carrasco's 80th-minute strike.
Barcelona remain five points off top spot with a game in hand after coming on strong late on to beat struggling Getafe 5-2.
Lionel Messi gave Barca an early lead and despite a Clement Lenglet own goal pulling Getafe level, a Sofian Chakla own goal and a second from Messi looked to have sealed the points for the hosts.
Enes Unal's 69th-minute penalty reduced the deficit before two goals in the last four minutes from Ronald Araujo and an Antoine Griezmann penalty wrapped up the win.
Real Sociedad ended a run of five league games without a win with a 2-1 success over Celta Vigo, while Granada beat bottom club Eibar 4-1.
Ten-man Atalanta extended their unbeaten run to six matches but missed the chance to move into second place in Serie A after being held to a 1-1 draw at Roma.
Ruslan Malinovskyi gave the visitors an early lead but Atlanta full-back Robin Gosens was sent off for a second yellow card and former Atlanta midfielder Bryan Cristante struck a long-range equaliser.
Lorenzo Insigne's seventh-minute penalty paved the way for Napoli's 5-2 win over Lazio, with further goals from Matteo Politano, Insigne again and Dries Mertens easing the hosts into a 4-0 lead just after the hour mark.
Goals from Ciro Immobile and Sergej Milinkovic-Savic briefly roused the hosts but an 80th-minute effort from Victor Osimhen sealed Napoli's win.