Real Madrid experienced bitter disappointment in the city derby at Atlético after five wins from five games and lost their lead in La Liga.
After the 1:3 (1:2) defeat, the Spanish football record champions are now only third with 15 points behind arch-rivals FC Barcelona and surprise team FC Girona (both 16).
2014 world champion Toni Kroos scored the only goal for the Royals (35th), Alvaro Morata (4th/46th) and Antoine Griezmann (18th) scored for the local rivals.
Atlético improved to fifth place with its third win.
National player Antonio Rüdiger played through Union Berlin’s Champions League group opponents, Kroos was substituted in the 70th minute.
Real beat the Bundesliga club 1-0 at the start of the premier class on Wednesday.