The last-32 match could have been a fairytale away win for the 'Citizens' as they made an excellent start to the match.
Centre-back Gemma Bonner was on hand to head in a corner from Caroline Weir to give the visitors the lead in the first period.
After the first goal goalkeeper Karen Bardsley had to show her quality to keep out efforts from Amanda Sampedro and Ludmila Da Silva as Atletico looked to come back in to the match.
However, all of their good work was undone when Kenti Robles had a cross reflected in to the net to give Atletico a foothold back in the tie, and deny City a potentially momentous victory.