Diego Costa gave Atletico the lead in the 73rd minute but the visitors equalised with an own-goal by Atletico goalkeeper Miguel Angel Moya and secured the victory with a strike by Joaquin Correa after a breakaway in the 88th.
The second leg is next week in Seville.
Atletico were debuting their attacking trio of Costa, Antoine Griezmann and Victor ‘Vitolo’ Machin, a former Sevilla player, but they were not able to get the job done in an entertaining match in which both teams created many scoring chances at the Wanda Metropolitano Stadium.
‘It was an open match, but they capitalized on their chances,’ Atletico coach Diego Simeone said. ‘They deserved the victory.’
The result ended Atletico’s four-game winning run.
Moya tapped in Sevilla’s equaliser after a cross by midfielder Jesus Navas deflected off the leg of defender Lucas Hernandez and went over the goalkeeper toward the top corner. It wasn’t clear if the ball would have gone in if Moya hadn’t touched it.
Navas had entered the match five minutes before the goal.
Correa netted the winner after a late breakaway, entering the area and flicking the ball past Moya as the goalkeeper charged out to try and block.
Costa had a chance to score an equaliser in injury time but couldn’t get a shot off from close range. He had a goal disallowed early in the first half because of a foul by Griezmann on a defender off the ball.