Lucas Paqueta had given the visiting team the lead after 54 minutes, before Neymar equalized from the penalty spot just over 10 minutes later.
However, the game’s main talking point came when Pochettino opted to replace Messi with right back Achraf Hakimi with 15 minutes of the match still remaining, seemingly to the six-time Ballon d’Or winner’s chagrin.
Pochettino and Messi didn’t shake hands and the pair had a brief exchange as Messi made his way to the bench.
PSG went on to win the Ligue 1 clash thanks to a Mauro Icardi header from Kylian Mbappé’s cross in stoppage time and Pochettino defended his decision to replace Messi.
“I think we all know we have great players in this 35-man squad,” Pochettino told reporters. “Only 11 can play, we can’t play more. The decisions in the game are made for the good of the team and each player.
“Every coach thinks about that. Sometimes it works, sometimes it doesn’t. Sometimes players like it and sometimes they don’t. At the end of the day, that’s why we’re here.
“These are decisions that have to be made by the coach. As for his reaction, I asked him how he was, he said he was okay. That was it. That was our exchange.”
Messi looked lively at times during the match — hitting the woodwork with a free kick and bringing a smart save out of Anthony Lopes — but PSG’s marquee signing still looked far from being the player fans had become used to seeing at Barcelona.
The fearsome front three of Messi, Neymar and Mbappé will no doubt need more time to gel, but Sunday’s game provided glimpses of the threat they could become.