Porto started the game well and they came close to opening the scoring when Jackson Martinez volleyed against the crossbar after being gifted space inside the box by the hosts.
Atletico managed to break the deadlock with their first clear opportunity, as Raul Garcia earned himself some room in the penalty area before firing in the opening goal from a tight angle.
The visitors continued to threaten as they searched for the victory they needed, with Silvestre Varela hitting the crossbar with a header from close range.
Daniel Aranzubia was adjudged to have fouled Martinez after coming off his line to challenge the forward, and Porto were handed a great chance as the referee pointed to the penalty spot.
However, Josue failed to find the corner of the net with his effort from 12 yards and Aranzubia reacted well to make up for his mistake moments earlier.
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Porto's frustration continued when Martinez hit the woodwork again with a deflected effort.
Diego Costa piled the misery on the visitors just a few seconds later as he sprinted clear of the Porto defence to take the ball past Helton and score a second goal for his side.
Despite needing three goals to stand any chance of qualifying, Porto continued to look dangerous in the second half of the match in the Spanish capital.
Lica came off the bench for the away side but Porto's bad luck in front of goal continued when the forward struck the post from a tight angle.
Atletico secured the result as they killed the game off with apparent ease in the closing stages to send Porto out of the competition.