In a dramatic finish, Atletico were denied a penalty when the referee studied the VAR and decided Jota had not fouled Jose Maria Gimenez.
The Reds are top of the Group B with three wins out of three while Atletico are equal on four points with Porto , who beat AC Milan 1-0 in Portugal.
Much of the night's drama happened at the Wanda Metropolitano in the Spanish capital were Mohamed Salah scored another impressive goal, twisting away from a string of Atletico Madrid defenders before his shot deflected in off James Milner to open the scoring.
Naby keita doubled Liverpool's lead with a stunning volley but Atletico hit back with French international Antoine Griezmann scoring twice to fire up the home crowd.
Just as Atletico Madrid seemed to have the upper hand, Griezmann was given a straight red card for a high boot in the face of Roberto Firmino.
A pulsating game was decided from the penalty spot in the 78th minute as Salah sent Jan Oblak the wrong way after Mario Hermoso pushed Diogo Jota. The Egyptian's 31st Champion League goal makes him the club's top scorer in the competition, overtaking Steven Gerrard.
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