With the Argentina ace deemed only fit enough for a place on the bench following his hamstring injury in the first leg, Barcelona lacked their usual swagger and PSG took a deserved lead in the 50th minute through Javier Pastore.
But the introduction of Messi in the 62nd minute changed the mentality and belief of the home side, with their talismanic forward the architect of Pedro's equaliser just nine minutes later.
Former England captain David Beckham was another star name who had to make do with a place among the substitutes having started last week, with Marco Verratti and Thiago Motta selected in central midfield as Blaise Matuidi was suspended following his yellow card at the Parc des Princes.
Xavi had a number of the home fans in Camp Nou on their feet in only the second minute as his free-kick curled up and over the wall and away from the diving Salvatore Sirigu only to ripple the side-netting, and that was as close as they came in a rare 45-minute spell where they failed to get a shot on target.
As ever, there was plenty of possession for the home side, but their passing lacked penetration and Victor Valdes was by far the busier of the two goalkeepers in the first half, with Lucas providing the main threat for the visitors with his powerful runs.
The Barca goalkeeper had to be alert in the 14th minute to deny Lucas' low drive from the edge of the box and was called into action again as the half-hour mark approached to push a powerful header from the Brazil international up and over the bar after an excellent deep cross from Ibrahimovic.
PSG took a deserved lead in the 50th minute after a lightning counter-attack with Zlatan Ibrahimovic linking superbly with Pastore, although the chance looking to have gone as the latter took the ball wide before lifting his shot over Valdes and into the net.
Pastore had a chance to double their advantage eight minutes later when he was again played in by Ibrahimovic, only to skew his shot horribly wide, with Barca coach Tito Vilanova turning to Messi to change the game.
His arrival lifted the crowd and his team-mates, with Andres Iniesta cutting into the box after a one-two with David Villa before curling in a shot which Sirigu pushed away and Messi could not get the rebound out from under his feet.
But there was no stopping the diminutive ace in the 71st minute as he unlocked the PSG defence to feed David Villa, with the forward rolling the ball back into Pedro's path to drill his shot home.
Carlo Ancelotti turned to Beckham as the clock ran down but his only contribution was to pick up a booking for dissent, with another moment of Iniesta magic seeing Barcelona go close as he turned Christophe Jallet inside and out before drilling into the side netting.