On his home debut for his new club, Messi was taken off 14 minutes from time for Achraf Hakimi as PSG chased a winner.
Neymar’s penalty had cancelled out Lucas Paqueta’s opener for the visitors but Messi, who struck the post with a free kick earlier in the game, looked bemused when the fourth official’s substitution board showed his number in the 76th minute.
Substitute Mauro Icardi scored a late winner for Pochettino’s side in stoppage time to take PSG five points clear of Olympique Marseille at the top of the table.
Asked why he decided to substitute his compatriot, Pochettino said: "Everyone knows we have great players on the team.
"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."
PSG are back in action on Wednesday when they travel to Metz.
