Messi gingerly walked off the Camp Nou pitch in the 58th minute, just moments before Atletico substitutes Angel Correa and Fernando Torres went on and linked up to equalize.
The defending champions said Messi will be sidelined for three weeks with a groin strain.
"With Leo Messi out, football loses, we all lose," Barcelona coach Luis Enrique said. "We now have to look for different solutions. Of course we are stronger with Messi, but we are still strong enough."