Messi opened the scoring in the 38th minute but spent the final moments of the first half standing motionless by the touchline and was replaced at the interval by Cesc Fabregas.
The Argentina international will undergo a scan on a suspected hamstring injury in his right leg on Wednesday with the return meeting against PSG already on the horizon on April 10.
Defender Javier Mascherano is certain to miss the second leg after he was forced off in the closing stages at the Parc des Princes, with assistant coach Jordi Roura confirming the former Liverpool man is facing several weeks out.
Roura said: "I think it was a typical quarter-final and a good result but we deserved better. It comes at a price because we have lost Messi as well as Mascherano, who will be out for four to six weeks."
Messi's opener was cancelled out by Zlatan Ibrahimovic, with Xavi restoring Barcelona's advantage late on from the spot, only for Blaise Matuidi to snatch a last-gasp leveller.
Fabregas confirmed Messi had been left despondent by the injury, but has backed his team-mate to be back on the field as soon as possible.
"He is down, obviously, because he is injured," Fabregas told Sky Sports News. "He hasn't been injured for many years and has played a lot of football for the last five years, so he is sad obviously.
"I know him very well, so he will just want to recover as soon as possible."
He added: "It was a very good game, they are a very good side and have quality players. It is not a bad result but we scored in the final minute of the game so we expected to win, so we are a little bit sad.
"We play at home (in the second leg) we always have options there. But when you score in the last five or 10 minutes you want to defend well and then from a rebound we conceded so it was unfortunate."