The visitors went one goal ahead on 37 minutes through Maxi Rodriguez before Steven Gerrard converted from the penalty spot in injury time.
The drew puts Atletico level on points with eight minutes in the group's first spot after each team played four games so far.
Liverpool didn’t look at their best, and the hosts took full advantage eight minutes before the end of the half courtesy of Maxi's strike.
The Argentine received Antonio Lopez's low cross with a brilliant first touch to nutmeg Jamie Carragher before firing his shot past Giuseppe Reina.
The hosts tried their best to equalize but all their efforts were in vain in front of a resilient Atletico backline.
Just as everyone thought the three points were heading to Madrid, Liverpool were awarded a penalty after what seemed a fair tackle from Mariano Pernia on Gerrard.
Atletico players were absolutely furious with the decision and four players were cautioned for protests, but that didn’t stop Gerrard from scoring the equalizer.
In another game, Marseille won their first points of the competition after easily beating PSV Eindhoven at the Stade Velodrome.
Ivorian Bakari Kone broke the deadlock for Marseille on 30 minutes after a lovely set up by Hatem Ben Arfa, and a second half brace from Mamadou Niang sealed the big win for the hosts.
Both Marseille and PSV are now third and fourth of group D respectively with three points each.