The Reds were headed for defeat, with Joao Felix's seventh-minute header looking like settling the first leg at the Wanda Metropolitano.
Diego Simeone's side were well on top and could have counted themselves as unfortunate not to be leading by more, having hit the woodwork in the first half and again after Anthony Elanga scored a brilliant 80th-minute equaliser.
The Swede came off the bench to score for the second time in four days, as he coolly slotted past Atletico's giant Slovenian goalkeeper and captain Jan Oblak.
It was a great finish but we shouldn't forget the sliderule pass from Fernandes and the Portuguese playmaker has now become the first player in Champions League history from an English club to assist a goal in six consecutive appearances.