They took the lead after only four minutes when former Real Madrid forward Morata converted Samuel Lino’s dangerous cross.
Antoine Griezmann then added another header to make it 2-0, before Toni Kroos’ superb low strike cut the lead in half.
But Morata clinched Atletico’s triumph after the break when he rose highest to meet Saul Niguez’s cross.
Before this match, Atletico had only won one of their previous 14 La Liga Madrid derbies, but they startled their bitter rivals with two goals in the first 18 minutes and then defended resolutely thereafter.
England midfielder Jude Bellingham, who has been in fantastic form since joining Real Madrid in the summer, cut a dissatisfied figure throughout, culminating in a yellow card in stoppage time for a bad challenge on Angel Correa.
Nova88 Official Partnerships:
Official Asian Regional Partner – Inter Milan
Introducing Nova88’s Official Partner in Asian Sportsbook Forum – Asianbookie
Nova88’s Official Partner Livescore Platform – Livescore.com