Playing at Jose Alvalade Stadium in Lisbon, Daniel Olmo made the score 1-0 for the Bundesliga club in the 50th minute.
Atletico’s Portuguese wonderkid Joao Felix equalized the game in the 71st minute.
A late goal by Tyler Adams brought victory for the German club in the 88th minute and RB Leipzig qualified for the next round.
Leipzig will face Paris Saint-Germain in the semifinals.
More about: UEFA ChampionsLeague