Argentina lost 2-0 at La Bombonera, their first defeat since lifting the 2022 World Cup.
Asked about Uruguay midfielder Manuel Ugarte's obscene gesture directed at Argentina midfielder Rodrigo De Paul in the 23rd minute of the game, Messi said: "Well, these young people have to learn. They [Uruguay] have a good group of players, a good national team, but they have to learn respect from their [Uruguay] elders because this Clásico was always intense, hard, but always with a lot of respect. So they have to learn a little."
Ugarte, 22, played down the episode, saying after the game: "These are things from the game that remain there. Now we have to enjoy."
De Paul had in the 19th minute been involved in an altercation with Uruguay defender Mathías Olivera that led to a brawl breaking out between the sides.
"It's normal, in this type of games, qualifiers, it's always like this with Uruguay," Messi said. "We knew what type of game we were going to find, it was difficult for us to play. They are intense and have physical and fast people. We did not feel comfortable."