The Liga side took the lead in the first half through Angel Correa, but they were left pointless after Nicolas Gaitan inspired an impressive Benfica fightback
Goals from Nicolas Gaitan and Goncalo Guedes secured a surprise 2-1 Champions League win for Benfica over Atletico Madrid as the Portuguese side took early control of Group C.
The visitors headed to Vicente Calderon having failed to win on their travels this season or beat Spanish opposition in Europe since 1982.
But after falling behind to Angel Correa's 23rd-minute effort, Rui Vitoria's men - who beat Astana on matchday one - struck back either side of the break and survived a late onslaught from the hosts to clinch a potentially vital victory.
Atletico coach Diego Simeone had identified Gaitan as Benfica's main threat in the build-up to the game and will therefore have been disappointed by the way his charges allowed the Argentina midfielder to drift in unmarked at the back post to draw his side level.
And the home defenders failed to heed the warning as it was Gaitan who provided a delightful assist for what proved to be the winner from Guedes.
The 2014 beaten finalists threw everything they had at the visitors in the latter stages, but a combination of poor finishing and some fine saves from Julio Cesar ensured they tasted defeat for just the fourth time in their last 25 home European ties.
In what was a pulsating tie, the goalmouth action started almost immediately.
In-form Benfica striker Jonas beat three defenders on a mazy dribble before dragging his shot wide six minutes in, while Tiago's goal-bound effort was deflected wide at the other end moments later.
The visitors went close again when Guedes beat Jan Oblak to a ball on the edge of the Atletico area, but saw his curling shot cleared off the line by Filipe Luis who was perfectly positioned to spare his goalkeeper's blushes.
A volley from Jackson Martinez that looped over the bar was Atletico's immediate response, but they were not to be denied for long.
Antoine Griezmann has been in sparkling form for the Spanish side this season and the Frenchman provided the cushioned assist for Correa who gleefully rifled past Julio Cesar from close range.
The Liga side came agonisingly close to doubling their advantage soon after as Martinez struck the woodwork and was then foiled by Cesar having been picked out by another fine cross from Griezmann.
With Atletico rampant it seemed inevitable they would extend their lead before the break, but Benfica retained some threat on the counter-attack and managed to level matters in the 36th minute.
The hosts failed to deal with a ball driven in from the right by Andreas Samaris, allowing it to travel all the way across the box to the far post where the onrushing Gaitan slammed it first time past Oblak.
Simeone's men made a strong start to the second half, only to be undone by a classic sucker punch as Gaitan got away down the left, picked out Guedes and the Portugal Under-20 international steered home at the far post.
Shortly before the hour mark, Benfica were indebted to Cesar as he produced a stunning double save to deny Martinez and Correa, while a fine block from Luisao kept out a goal-bound strike from the luckless Martinez moments later.
Simeone introduced Fernando Torres for the final quarter, but the former Chelsea man was unable to bag what would have been his 100th goal for the club as the visitors hung on for maximum points.