Rafael Benitez’s side were put to the sword 4-0 by in Saturday’s Clasico at the Santiago Bernabeu and they now suffer the added humiliation of slipping below their near neighbours in the standings.
Koke’s first goal since August’s 3-0 win at Sevilla was just reward from an enterprising start by Atletico and Antoine Griezmann and Yannick Ferreira Carrasco might have extended their advantage before the break.
The second half was more attritional in nature, although Diego Godin led by example with some brave defending that left the hosts frustrated.
Atletico are four points behind Barcelona on 26 and two better off than Real, who drop to third.
Players and fans paid tribute to the victims of the Paris terror attacks ahead of kick-off and an Atletico starting XI featuring Griezmann, the France forward whose sister survived the siege at the Bataclan theatre last Friday, went ahead after seven minutes.
Recalled Betis midfielder Xavi Torres was hustled out of possession dangerously close to his own penalty area and Atleti striker Fernando Torres fired in a low shot that Antonio Adan saved but Koke dispatched the rebound.
Betis looked to press their opponents back but the confident swagger of Atletico’s play was evident when Fernando Torres exquisitely chipped a pass over the home defence with the outside of his foot and Griezmann crashed a volley over.
Alfred N’Diaye sought to drive Betis forward from midfield and sent a speculative drive over, although Pepe Mel’s team were unable to craft clear-cut chances before half-time.
They should have been further behind when Koke played Carrasco in behind the Betis defence, only for the Belgium international to fire into the side-netting.
Xavi Torres made way for Dani Ceballos at the break and his namesake Fernando was denied by a timely Heiko Westermann challenge having made a mazy run into the box.
A sickening clash of heads between Godin and Adan left the both men bloodied and the goalkeeper was eventually forced off having landed awkwardly in the challenge.
Atletico keeper Jan Oblak was at full stretch in the 59th minute to tip a vicious swerving strike from Alvaro Cejudo over before Godin received another heavy blow to the head as N’Diaye tried to convert at the back post.
Griezmann had a chance to settle Atletico nerves in the 73rd minute but spurned time and space inside the Betis area to lift a shot over.
The Frenchman had a strong penalty claim waved away when Westermann slid in clumsily before he clipped the post with stoppage time approaching, but Griezmann’s personal frustrations in front of goal were soothed by three hard-earned points.