Luis Suarez headed the first-half winner to hand Atletico manager Diego Simeone victory in his 500th game in charge of the club.
Atletico is two points clear of rivals and defending champions Real Madrid, who were held to a 1-1 draw at Elche.
Simeone’s side, who are chasing a first league title since 2014, has won 301 matches under his tenure.
The club parted company with striker Diego Costa on Tuesday after the Spain international fell out of favour at the club.
Suarez and Joao Felix have been preferred to Costa up front this season, and Simeone will feel vindicated in his decision as the former struck the decisive blow against Getafe.