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After coming on as a substitute in the 60th minute, Messi scored Argentina's third goal from a free-kick in the 80th minute, taking his tally to a record 19 goals across all of his FIFA World Cup appearances.
Scaloni made nine changes to his starting line-up compared with the previous match, in which the reigning world champions defeated Austria 2-0.
Scaloni said the 39-year-old Messi "could have played the full 90 minutes today, but he also preferred that his teammates get playing time and wanted to think about what lies ahead."
He added: "That reflects his personality in the best possible way, because he doesn't think about the records people talk about so much."
Messi, captain of the Albiceleste, became the first player to score in seven consecutive FIFA World Cup matches.
Scaloni continued: "I'm happy he made that decision. When I spoke with him, he said it was the best option, and I agreed. I think it shows just how much the Argentina national team means to him, as well as the group and his teammates. That's truly wonderful."
He concluded: "No one can take away what he has achieved, but there is nothing left for him to add."