Diego Simeone's men close to within four points of leaders Barcelona, but now lead city rivals Real Madrid by two points after Barca thrashed Real 4-0 on Saturday.
The visitors were rewarded for a fast start as Antonio Adan could only parry Fernando Torres's shot on seven minutes and Koke was on hand to sweep home the rebound.
Atletico should have gone on to win by a much greater margin as they controlled the game throughout.
Bernabeu stunned: Real beaten red and blue
Antoine Griezmann volleyed Torres's lovely chipped past over midway through the first half.
Betis only threatened to strike back once when Jan Oblak produced a stunning save from Alvaro Cejudo's long-range effort.
Griezmann missed an even better opening to kill the game when he blazed over with Koke begging for a cut-back to slot into an open goal after the break.
However, the Frenchman was very unfortunate moments later when he was clearly brought down inside the area by Heiko Westermann, but the referee waved play on.
Zidane in "no rush" to coach Real Madrid
And Griezmann's night in front of goal was summed up when he struck the inside of the post three minutes from time.
Elsewhere, Villarreal edged into the top four on goal difference thanks to a Jaume Costa late equaliser in a 1-1 draw at home to 10-man Eibar.
Granada moved out of the relegation zone with a 2-0 win over Athletic Bilbao, and Levante also edged closer to safety with just their second win of the season, 3-0 away at Sporting Gijon.
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