The five-time World Player of the Year missed Argentina's World Cup qualifier with Venezuela earlier this month due to the problem and only started Barca's shock 2-1 defeat to Alaves 10 days ago on the bench as coach Luis Enrique bedded him back into action gently.
Messi's absence had an immediate impact as Angel Correa scored for Atletico just a minute after his international teammate went off to level the scores at 1-1.
Barca pushed for a winner after Correa's equaliser, but could not find that vital goal and Luis Enrique would have probably loved his star man to be on the pitch for the closing stages of the game.