The Reds faced Diego Simeone's men at Anfield on March 11 in the second leg of the sides' last-16 tie.
Trailing 1-0 on aggregate from the first fixture in Madrid, the hosts took a 2-0 lead on the night through goals from Georginio Wijnaldum and Roberto Firmino, the latter coming in extra-time.
However, a Marcos Llorente brace and a further strike from substitute Alvaro Morata sent Atleti through to the next round.
Liverpool's two goals were met with celebrations that involved the setting off of pyrotechnics, and Uefa's control, ethics and disciplinary board have taken action as a result.
The Merseyside club have subsequently been hit with a small fine that must be paid within the next 90 days.
Defeat to Atletico was Jurgen Klopp's side's last outing prior to the coronavirus pandemic forcing the suspension of football in the United Kingdom.
Madrid's status as a centre of the spread of Covid-19 has prompted criticism of Uefa and the UK government for allowing the fixture to go ahead.