An attacking line-up of Beth England, Sam Kerr, Fran Kirby and Pernille Harder showed the away team’s desire to put the tie beyond doubt rather than defend their hard-earned first-leg lead.
The positive approach almost worked early on, Harder narrowly off target with a rasping 25-yard effort and Kirby shooting over on the follow-up after Kerr’s low cross was almost diverted in to her own net by Grace Kazadi.
But the hosts were the more threatening thereafter, with the pace and direct running of Ludmila and the quality of Duggan posing regular problems.
Duggan had two decent long-range efforts on goal, the first going just over and the second forcing a fine stop from Berger.
Atletico’s pressure continued to build in the second half but Millie Bright and Mjelde stood firm at the heart of an overworked defence thanks to a combination of some fine defending and generous refereeing.
The two penalties that were were awarded brought a frantic finish but Chelsea managed to stay calm enough to progress and keep alive their hopes of a first Champions League success.