The Vicente Calderon outfit have released an official statement to condemn the events during last week's Primera Division fixture
Puerta tragically died in August 2007, and the Madrid-based side have now condemned the disgraceful behaviour of some of their fans.
"Atletico Madrid deeply regret the chants aimed at Antonio Puerta during the match this past Sunday, the 2nd of October at the Vicente Calderon Stadium," the statement reads.
"Our club is deeply repulsed by these songs and apologises to the family of the late footballer, to Sevilla and to the general football public.
"Atletico Madrid support respect in football and we hope that these actions are not repeated at our stadium or in any other of our football grounds."
Puerta passed away at the age of 22, three days after succumbing to heart failure in the match against Getafe on August 25, 2007.