The Portuguese side and Chelsea were already through to the knockout stages of Europe's top club competition and APOEL Nicosia needed a win in London to claim third place in the group and the lucrative Europa spot. They fought hard but had to settle for a 2-2 draw.
Atletico were hoping for a return to form in Europe after two straight La Liga wins but fell behind in only the second minute at the Calderon.
Bruno Alves leaped above the home defence to head in from a corner and Radamel Falcao made it two 12 minutes later when he rifled home the rebound from a long-range Fucile strike.
Diego Forlan and Cleber Santana then missed chances for Atletico before an acrobatic effort from Sergio Aguero slammed into the side netting.
The referee earned the wrath of the home fans shortly before halftime when he turned down a Simao Sabrosa penalty appeal and then booked the Portugal winger for diving.
Atletico looked woefully short of ideas going forward in the second period, particularly after striker Aguero limped off just after the break with a thigh injury.
When Hulk smashed in a third off the crossbar in the 76th minute some disgruntled fans began heading for the exits and the handful remaining at the whistle roundly booed the home side.
COMFORT ZONE
Atletico coach Quique Sanchez Flores, who said he had not been following the score of the match at Stamford Bridge, complained that his players had been second to every ball which had made it impossible to claw their way back into the match.
"It's very hard to pull back two goals conceded in 15 minutes against a very physical team that is playing in its comfort zone," he told a news conference.
"The fans are very demanding and that's the way it should be. They were expecting a better performance."
Undefeated Chelsea topped the group with 14 points from six matches ahead of Porto on 12, and Atletico and APOEL with three.
Competition rules enabled Atletico, who conceded five more goals than the Cypriot side and scored only three to APOEL's four, to go through to the Europa League thanks to Simao's goal in last month's 1-1 draw in Nicosia.
