Atletico reopened the three-point gap ahead of Real Madrid after their rivals beat Almeria 4-0 on Saturday, but an injury to Diego Costa initially overshadowed their away win.
The 25-year-old - who was returning from a hamstring strain – crashed into the post while scoring, appearing to take a heavy blow to his left leg, and he was subsequently carried off on a stretcher in clear discomfort.
Although Atletico later confirmed Costa only suffered a cut, it is still likely to be a concern for coach Diego Simeone at such a crucial time of the season.
The table-toppers clinched a UEFA Champions League semi-final place on Wednesday by defeating Barcelona and they prevented a European hangover when Diego Godin nodded them into a first-half lead.
Costa's goal came after he had already missed a penalty, with Angel Lafita's red card compounding a difficult day for Cosmin Contra's relegation-threatened Getafe.
In Andalusia, Sevilla made the short trip across town to beat bitter rivals Betis 2-0.
Unai Emery's men thumped Porto 4-1 in Europe's second-tier competition on Thursday and although they were full of confidence after booking a place in the semi-finals, they had to rely on luck on Sunday as they won a controversial penalty in the 27th minute.
Juan Carlos received a straight red card for hauling down Carlos Bacca in the penalty area, but replays showed the Spaniard won the ball fairly. Kevin Gameiro then coolly converted the spot-kick for Sevilla.
Betis coach Gabriel Calderon claimed he had "never seen this level of refereeing" after the match and his side were finally put out of their misery eight minutes from time as Gameiro netted his second.
The win leaves Sevilla three points behind the fourth-placed Athletic Bilbao – who play Malaga on Monday – and Betis stay rooted to the bottom, 10 points adrift of safety with five matches to play.
Valencia's slim chances of earning a UEFA Europa League spot for next season remain alive thanks to a 2-1 over Elche, leaving them seven points behind the seventh-placed Real Sociedad.
Coro netted in the 28th minute to cancel out Pablo Piatti's opening goal, but the hosts clinched the win thanks to Dani Parejo just after the hour-mark, despite Antonio Barragan receiving a second yellow card in stoppage time.
Damian Suarez missed a second-half penalty for the losers, who are just four points above the relegation zone.
The day's other match saw Espanyol salvage a point in a 2-2 draw against Rayo Vallecano. Defender Diego Colotto was Espanyol's hero, heading in a corner with just two minutes left.
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