The Portuguese side recorded their first-ever win in the Europa League with a shock 2-0 victory over Los Colchoneros, whose year-long run came to an abrupt end
The hosts took the lead through Wilson Eduardo's fine finish just before the half-hour mark, before the forward struck home a penalty in the second half and confirmed a famous win, as a poor and disjointed Atletico side were put to the sword in Coimbra.
In a cagey opening in Portugal, los Colchoneros' shuffled squad took a while to get into their rhythm as they were matched by a determined Academica side in the early stages. The likes of Jorge Pulido, Cata Diaz and 17-year-old Saul Niguez were handed run-outs.
Raul Garcia almost gave Diego Simeone's side the lead after a defensive lapse allowed the chance to be created, though the midfielder was to be denied by a near-heroic block by Joao Real, whose intervention prevented the ball from beating the goalkeeper.
Academica then proceeded to continue to test the visitors, as Wilson Eduardo's speculative delivery was somehow awkwardly punched away by Sergio Asenjo - in the side ahead of Thibaut Courtois - with Cleyton failing to get a clean hit on the rebound.
Nevertheless, Pedro Emanuel's side took the lead in what essentially was the first real chance of the game. From a throw-in, Joao Dias' measured cross was well adjudged by Eduardo, who ghosted in front of Silvio to gently divert the ball with a fine left-foot touch past Asenjo into the net.
The opening goal sought to invigorate the hosts, and woke up the defending champions, who by that point endured a very poor half-hour. Academica did enough to hold onto an interval lead, in a first-half with very few chances as the Spanish side's 16-game winning streak looked under serious threat.
The second half started much more positively for Atletico with Koke racing forward and firing a dipping shot from distance, which goalkeeper Ricardo needed to tip around the post, just 30 seconds into the period.
Simeone's men continued to force through an opening, but were kept at arm's length by a determined Academica side who were fighting for Europa League safety.
Moments after Emre came on for Mario Suarez, the Turkey midfielder struck the woodwork with a fine effort which left the goalkeeper confused before Pedro Martin and Raul Garcia failed to find the net with unsuccessful efforts.
The game-changing moment happened in the 70th minute when Jorge Pulido was adjudged to have felled Salim Cisse in the penalty box, with English referee Lee Probert awarding the penalty. Up stepped Wilson Eduardo to send Asenjo the wrong away, and give the hosts a 2-0 lead.
Atletico continued to look for a goal, as Adrian attempted to dribble his way on the wing, but the Portuguese side held on to record their first ever win in the Europa League and hand the visitors a first defeat in this competition since October 2011.
Simeone's side stay top of the group with nine points, despite Viktoria Plzen's crushing win over Hapoel Tel-Aviv, They host Getafe when La Liga resumes on Sunday and encounter Hapoel on matchday five.