The match, played in front of 80,000 passionate fans at Estadio Monumental, marked what is expected to be the 38-year-old's final competitive appearance in Argentina.
Messi opened the scoring in the 39th minute with a deft chip over the onrushing goalkeeper after a clever pass from Julian Alvarez. Lautaro Martinez added a second in the 76th minute before Messi sealed the result four minutes later with his second goal when he tapped in from close range.
Speaking after the match, the 38-year-old reflected on the significance of the moment.
"Being able to finish this way here is what I've always dreamed of. I've experienced a lot of things on this pitch, both good and not so good, but it's always a joy to play in Argentina, in front of our fans," Messi told TyC Sports.
"For many years I had the affection of Barcelona, and my dream was to have it here too, in my country with my people. A lot of things were said, but I'll stay with all the good."
Despite the vintage performance, the eight-time Ballon d'Or winner expressed uncertainty over his participation at the 2026 World Cup in the United States.
"Same as I said before about the World Cup - I don't think I'll play another. Because of my age, the most logical thing is that I won't make it," he admitted.
"But we're almost there, so I'm excited and motivated to play it. I go day by day, match by match, trying to feel good and, above all, being honest with myself. When I feel good, I enjoy it. But when I don't, honestly, I don't have a good time, so I prefer not to be there if I don't feel good.
"I'll finish the season, then I'll have pre-season, and there will be six months left. So we'll see how I feel. Hopefully I'll have a good pre-season in 2026, finish this MLS season well, and then I'll decide."