The Argentine legend made his home debut for his new club, but is still yet to score for them as they secured a last-gasp victory with him sat on the bench.
Messi hit the post from a free kick and saw a one-on-one saved by Anthony Lopes in the first half.
In the second period, Lucas Paqueta broke away and gave the visitors a surprise lead on 54 minutes.
Not long later though, Neymar was brought down in the box and it appeared as though Messi's moment was about to come.
However, in a surprise to some, it was Neymar himself who took the spot kick and finished it with aplomb to bring the game level.
With the game tied at 1-1 and just 15 minutes remaining, all four of Messi, Neymar, Kylian Mbappe and Angel Di Maria were still on the field.
In another surprise, Messi was the first to make way.
Pochettino opted to bring on Achraf Hakimi in place of the legend who seemed to subtly show his displeasure with the decision as he walked off past his manager.
Ultimately, the match ended 2-1 as Mauro Icardi found PSG's winner after all, heading headed home in added time from Mbappe's cross.
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