Barca needed a Pedro equaliser in the 71st minute to draw 1-1 with PSG and advance to the last four on away goals.
Messi started on the bench at Nou Camp, after injuring his hamstring in last week's 2-2 first-leg draw in Paris.
Barca were lacking an edge without their talisman, and PSG looked dangerous in the first half.
Five minutes after the break Javier Pastore burst through the defence and lofted the ball over Victor Valdes into the net to make it 1-0 to the visitors.
The hosts were in danger of suffering their first Champions League loss at home since a 2-1 defeat to Russian side Rubin Kazan in October 2009.
However, Messi replaced Cesc Fabregas with half an hour to go and got involved straight away, being influencial in the build-up to Pedro’s goal.
The Spaniard, who was only cleared to play shortly before kick-off after a muscle injury, put in a clinical finish from the edge of the area.
With the win Barcelona earn a sixth straight semi-final appearance in Europe's elite club competition.