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Messi made the PSG starting XI alongside Neymar, Kylian Mbappe and Angel Di Maria for his side’s clash with Lyon at the Parc des Princes on Sunday.
Lucas Paqueta opened the scoring for Lyon early in the second half, but Neymar pulled back an equaliser after beating Anthony Lopes from the spot-kick.
Messi, who hit the woodwork from a free-kick, made way for Achraf Hakimi in the 76th minute as the Barcelona legend waits to open his goalscoring account for PSG.
However, the 34-year-old Argentine forward appeared to snub a handshake from Pochettino on the touchline as he was withdrawn from the Ligue 1 match.
Messi was forced to watch on from the sidelines as Mauro Icardi, who came off the bench to replace Di Maria in the 82nd minute, headed home the winner in injury time.
Speaking after PSG’s 2-1 win, Pochettino played down any suggestions of friction with Messi after the handshake snub.
“I took the decision to take Leo off to protect him for possible injuries. We have important games coming up and we want to protect him,” he said.
“These are decisions that we make for the good of the team. Everyone knows we have great players.
“We have a very rich squad of 35 players. Then we have to make choices. With the 11 who must start and then we have to make decisions during the game.
“Sometimes these choices pay off and sometimes they don't. But that's why we're standing in front of the bench thinking about what to do. And those decisions that you have to make, whether things go well or not. Whether you like it or not.
“Afterwards, Messi told me he was fine with the decision.”
Messi, who left Barcelona in the summer on a free transfer, made his PSG debut against Stade de Reims last month.
PSG maintained their unbeaten start in Ligue 1 this season and are top of the table after their opening six league matches.
Pochettino’s men will return to action on 22nd September for their Ligue 1 match with Metz at the Stade Saint-Symphorien.
Featured Image Credit: PA
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