Gareth Bale led the way without him, scoring the opening two goals.
Atletico Madrid coach Diego Simeone said he would not rest any players for Saturday's penultimate Liga game away to Getafe, even with the Europa League final against Olympique de Marseille coming up on Wednesday.
Atletico won the competition in 2009 and 2012 and went into the knockout stages of this year's tournament after finishing third in their Champions League group, but Koke refuses to see it as a consolation prize.
Villarreal and Sevilla clinched Europa League berths for next season. Los Colchoneros have bagged seven of the last 15 points available in the league, collecting wins over Levante and Alaves as well as suffering disappointing defeats over Espanyol and Real Sociedad.
Atletico goalkeeper Jan Oblak also saved a late penalty from Faycal Fajr as Diego Simeone's men warmed up for Wednesday's Europa League final against Marseille by denting Getafe's hopes of playing continental football next season.
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The Slovenian made another good save in stoppage-time, tipping a header over the crossbar to ensuring Getafe missed out on seventh place to Sevilla, denying them a return to Europe for the first time in a decade.
The Argentinian was hit with a four-match suspension after he was charged with insulting a match official during the first leg of his side's Europa League semi-final against Arsenal in London on April 26. Francisco "Isco" Alarcon, little-used defender Achraf Hakimi, and Toni Kroos added on, along with an own goal by Celta's Sergi Gomez, to ease to the big win at home.
Betis striker Loren bundled the ball in soon after Kjaer's strike to ensure his side will not have to play three playoff rounds to get into the Europa League.
El Geta now sit in eighth position in La Liga, two points behind Sevilla.