Angel Correa fired Atletico ahead in the 23rd minute at the Calderon when Antoine Griezmann cushioned a delightful pass into his path and he cracked the ball past Julio Cesar from close range.
Nicolas Gaitan levelled for the visitors in the 36th minute, smashing a first-time shot through a crowd of players, and teenager Goncalo Guedes made it 2-1 six minutes into the second half when he converted a Gaitan cross at the far post.
They were the first goals Atletico had conceded at the Calderon in Europe’s elite club competition in more than 700 minutes and prevented them from setting a Champions League record of eight consecutive home clean sheets.
Diego Simeone's side have won 21 of their last 25 European matches at home and it was their first defeat since a 2-0 reverse to Rubin Kazan in the Europa League last 32 in 2013.
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With two matches played, Benfica top the section with a maximum six points, with Atletico in second place on three. Astana and Galatasaray each have one point after they drew 2-2 in Kazakhstan earlier on Wednesday.
The game in the Spanish capital, the first competitive meeting between the sides, was marred by Benfica fans throwing flares towards the Atletico supporters after Gaitan’s equaliser.
(Reporting by Iain Rogers, editing by Pritha Sarkar)
