Marta became the first woman footballer to score in five consecutive Olympic Games.
The duo was together at Barcelona for four years before Neymar moved to Paris Saint-Germain.
Scaloni did not say what the injury was but he showered Messi with praise on a night Argentines took to the streets in huge numbers to celebrate their first international title in 28 years and Messi’s first victory with the national side.
Angel Di Maria netted the winner as Argentina beat hosts Brazil 1-0 at the Maracana to regain the Copa America after a long wait of 28 years.
The Super Sunday begins with arch-rivals Brazil and Argentina locking horns at the Maracana Stadium to be crowned champions of South America.
Brazil were on top in the first half but it took them 35 minutes to break the deadlock thanks to a side-footed volley from Paqueta after nice work by Neymar.
Brazil were unbeaten in 11 games and topped Group B, while Chile finished only fourth in Group A.
Peru take on Paraguay in the first quarterfinal.
The draw at an empty stadium in central Brazil marked the first time Brazil have not picked up a win since they lost 1-0 to Argentina in a friendly in November 2019.
Nestor Pitana, the Argentine who refereed the 2018 World Cup final, waved play on when the ball bounced off him outside Colombia's box and Brazil continued passing for Roberto Firmino to head in an equaliser.