Los Verdiblancos have taken a major step towards the top six after goals from Giovani Lo Celso and Sidnei secured three points in Seville.
Quique Setién’s side now occupy 7th place and are level on points with Levante, at least until Girona face a struggling Athletic Club on Monday evening.
A frustrating first half ended goalless before Lo Celso opened the scoring early in the second half.
The 22-year-old made no mistake from the penalty spot.
The goal sprung the away side into life as they committed men forward following the introduction of Raúl de Tomás from the bench.
The front three for Rayo, created several second half chances but failed to make them count.
Betis dominated possession, registering 60% to Rayo’s 39%, and unlike the visitors, made it count when Sidnei extended their lead with 15-minutes remaining.
At this stage, Míchel’s side looked deflated, and despite taking one last throw of the dice with the introduction of Bebé, they were unable to get back into the tie.
Los Verdiblancos were delighted to have talisman Sergio Canales back after his presence was sorely missed in their 1-0 victory over Real Sociedad last week.
As the game entered stoppage time, Bebé tried his luck from range but his attempt was well saved by Pau Lopez.
Rayo remain in the relegation places and are currently facing the prospect of being relegated at the first time of asking after promotion to La Liga last season.
Betis have now won their last four games in a row at home across La Liga, the Copa Del Rey and Europa League.
Next up in La Liga for Los Verdiblancos is another chance to set down a marker as they travel to the RCDE Stadium to face Espanyol.
Real Betis: (3-5-2) Lopez; Mandi, Bartra, Sidnei; Barragán, Canales, Carvalho (García, 83) Lo Celso, Firpo; Sanabria (León, 80) Loren (Joaquín, 70) Unused subs: Robles, Kaptoum, Inui, Tello.
Rayo Vallecano: (4-3-3) Dimitrievski; Advíncula, Gálvez, Amat, Moreno; Trejo, Comesaña (Medrán, 59) Imbula; Embarba (Bebé, 80), Pozo (De Tomás, 59) Garcia. Unused subs: García, Tito, Velázquez, Akieme.
Goal: Lo Celso (1-0, 58 pen) & Sidnei (2-0, 75)
Cards: (Yellows: Barragán, Carvalho, Medrán, Comesaña, Embarba)
Stadium: Estadio Benito Villamarin (40,218 attendance).