Brazil advanced to the final on Tuesday over their archrivals in a feisty, physical match at Mineirão stadium in Belo Horizonte, Brazil, with goals from Gabriel Jesus and Roberto Firmino. The hosts will face either Peru or Chile in Sunday's final at the Maracana stadium in Rio de Janeiro.
While the tournament has been plagued by lengthy stoppages for the video assistant referee (VAR), Ecuadoran referee Roddy Zambrano preferred to let the game run, which incensed Argentina when VAR did not come into play on several occasions.
"[The officials] were tired of making bulls--- calls at this Copa and they didn't go to VAR. It was unbelievable," Messi said after the loss.
"It was like that all match. It was bulls--- that they were doing it all match. There is no excuse -- it must be looked into. Hopefully, [South American football organising body] CONMEBOL does something about these kind of referees.
"Because we did everything to try and advance but [the officials] stacked the deck against us. I don't believe they will do anything because Brazil controls everything, so it is very complicated. But I don't think we should feel bad for anything. It didn't happen and we had bad luck."
On Wednesday, the Argentina Football Federation submitted a letter of complaint to CONMEBOL stating that they were "clearly harmed" by the officiating.
Messi, who still has not won a major title with Argentina, was more influential than in his first few matches here but was still a shadow of the player who had won everything with Barcelona.
"I'm upset because we had a great match, a great effort," the man from Rosario said. "It wasn't for it to finish in that way, because they weren't the better team."
Like his star player, Argentina coach Lionel Scaloni also complained about the referee's decisions.
"I didn't like the referee -- I don't usually make those comments," Scaloni said. "I don't think he was qualified for a match of this level."
Scaloni considered that in Firmino's goal, his team had heard a whistle in the beginning of Jesus' move. The Argentina coach was also unhappy with the fact that Argentina picked up six bookings to Brazil's two.
"If a midfielder player is on a yellow card, this changes things," he said. "There were a lot of small details where the match started to lose its balance because of those decisions."
Messi, who quit the national side after the 2016 Copa America final loss only to return for the 2018 World Cup, suggested he was still committed to the Argentina cause. The country will co-host the 2020 Copa America with Colombia, giving Messi another shot at a continental title.
"Something new is on the horizon," he said, adding that he hoped the fans back home would recognise the side's effort during the tournament.
"I hope we are respected and not criticised. They should let the team be and let them grow.
"The truth is, I have got on very well with this group of players, and if I have to help in some way, I will. This is a great group, which is growing, and if I can join them I will."
Information from Reuters and The Associated Press was used in this report.