Messi was left on the bench as he failed to fully overcome the hamstring injury suffered in the 2-2 first leg draw in Paris last week.
PSG took full advantage with the majority of goalscoring chances in the opening half before it went ahead five minutes after the interval through Javier Pastore.
Messi was summoned to the pitch on 62 minutes to the delight of the home fans, and the Catalan side lifted its intensity immediately.
The Argentine ace started the move that resulted in Pedro's equaliser on 71 minutes.
Barca progressed on the away-goals rule to join Bayern Munch, which accounted for Juventus 2-0 at home and 4-0 on aggregate, Real Madrid and Borussia Dortmund in a Spain v Germany final four.
The semi-final draw will take place on Friday evening (AEST) and you can see it LIVE right here on The World Game website.The Catalan side was far from its usual brilliant self without Messi and met its match in a disciplined and intelligent PSG, which afforded it little space and caused a lot of problems on the counter attack.
Cesc Fabregas began in place of Messi while Adriano was chosen at centre-back, deputising for the injured Javier Mascherano and Carles Puyol.
Xavi almost gave the host the dream start from a 30-yard free-kick, but his effort went just inches wide of the near post.
PSG did not take long to have its first attempts on goal.
A lively Ezequiel Lavezzi tested Barcelona goalkeeper Victor Valdes after two minutes and then raced towards goal after getting the ball from Sergio Busquets. He was stopped by Gerard Pique, who did exceptionally well to recover.
Iniesta tried an audacious lob from over 40 yards out as he saw Salvatore Sirigu off his line, but the ball sailed a couple of feet over the bar.
Lucas Moura then forced Valdes into a save, and a few moments later Lavezzi shot over the bar in a period of surprising superiority from the visitor, which was allowed a fair amount of possession of the ball and space.
Barca did not create another chance until 21 minutes, when Pedro forced a low save from Sirigu and the ball fell to the forward again, who hit the side netting.
Lavezzi then missed PSG's best chance of the half, forcing his way into the area but poking his shot straight at the legs of Valdes.
The goalkeeper had to be alert later on when Lucas headed the ball towards the top corner after a cross from the byline by Zlatan Ibrahimovic, but the Catalan stopper tipped it away for a corner.
Barcelona's first-half performance was well below its usual high standards, and although it had 13 shots on goal, could only hit the target once.
The second period initially followed the script of the first half, with Barca controlling possession but creating little danger.
The difference was that once PSG created a chance of its own, it made it count.
Ibrahimovic played Pastore in with a wonderful ball to the left-hand side and the Argentine surged forward ahead of Barca's line of defence, controlled the ball and clipped the ball into the net, over an oncoming Valdes.
Dani Alves had a chance to equalise shortly after the goal, but blazed over the bar, and then Pastore could have doubled the lead, but scuffed his shot wide from close range after a pass from Ibrahimovic.
With Barca needing to score and looking unlikely to do so, it brought on the man who has scored 51 times for it in the Primera Division and in Europe this season.
Messi was brought on in place of Fabregas, while Adriano, on a yellow card and carrying a knock, was replaced by Marc Bartra.
Messi had an immediate impact on Barca's spirit and gave it an edge in attack.
Sirigu had to dive low to stop an effort from Iniesta and the ball fell to Messi, who could not get his shot beyond the first defender.
Pastore then had a third effort, this time shooting just over the bar, before Barca pounced.
Messi created the danger on the edge of the area to play in David Villa before the ball landed at the feet of Pedro, who lashed the ball into the top corner.
It was only Barca's third attempt on target but it was struck with such power that Sirigu was left with no chance.
The goal allowed Barca to relax and forced PSG to come forward and attack.
It struggled in this new role and Carlo Ancelotti brought on David Beckham with seven minutes remaining to add to its creativity.
Barca coach Tito Vilanova took off Villa for defensive midfielder Alex Song as it sought to hold on and progress to the final four.
Barca breathed a huge sigh of relief when the final whistle sounded as it celebrated becoming the first team to qualify for the semi-finals of the Champions League six times in a row.
They will, however, be praying that Messi will be at full fitness when they do contest the final four of the competition, because they were a shadow of their usual selves without him and only stopped themselves exiting the tournament when he appeared.