Diego Simeone's side's strong second-half display brushed aside Miroslav Djukic's men at the Vicente Calderon, with Diego Costa's double - which moves him level with Cristiano Ronaldo at the top of the Liga scoring charts with 17 for the season - sandwiching a Raul Garcia strike.
Costa broke the deadlock with a superb individual effort just before the hour mark, before Garcia added a second with a fine left-footed finish five minutes later.
Costa then had one penalty saved by Diego Alves before scoring a second spot kick on 81 minutes, with his miss proving a minor negative for Simeone as a 4-0 win would have put Atletico above champions Barca on goal difference.
Elsewhere, Real Sociedad made it three Liga wins in a row with a 5-1 hammering of bottom-placed Real Betis.
Imanol Agirretxe opened the scoring after just six minutes at Anoeta, before Jorge Molina equalised for Betis to put the sides in level at the break.
However, a blitz of three goals in 13 minutes from Ion Ansotegi, Antoine Griezmann and Agirretxe put Sociedad firmly in control before Xabi Prieto sealed the victory five minutes from time - a result that means Betis have now gone nine top-flight games without a win.
Sociedad's latest victory moves them to within four points of fourth-placed Athletic Bilbao, who were held to a 1-1 draw at in-form Sevilla.
Alberto Moreno gave the hosts the lead in the fourth minute at the Estadio Ramon Sanchez Pizjuan, only for Markel Susaeta to draw Bilbao level just two minutes later.
Sevilla are now unbeaten in their last eight games in all competitions, while Bilbao have lost just one of their previous nine.
In Sunday's other Liga clash, Almeria and Espanyol played out a 0-0 stalemate at the Estadio de los Juegos Mediterraneos, with midfielder Verza missing a first-half penalty for the hosts.
