Argentina great Messi described the officiating in his side's Copa America semi-final loss to Brazil as "bulls***" and suggested his side were victims of "corruption" as he received a controversial red card in the third-place play-off with Chile, which led to a strong rebuttal from CONMEBOL who described his comments as "unacceptable" and "unfounded".
"Maybe I'm paying for what I said last time," the Barcelona star said.
Brazil defender Silva, responding to the comments, suggested Messi had benefited from such decisions in Barca's incredible 6-1 Champions League win over PSG two years ago.
"This is difficult for us to comment on," he said after Brazil's 3-1 final win over Peru. "Sometimes in defeat, we try to focus on other people.
"I think he did not say it out of spite, but we are sad because, in the game we lost 6-1 to Barcelona, he played the referee, which, in my opinion, was ridiculous.
"But we did not give a statement that the referee was in favor of Barcelona. I think you have to show respect.
"Brazil do not have five stars [from World Cup wins] at random - none of them have been stolen. It was played on the pitch."
Silva's PSG and Brazil team-mate Marquinhos added: "[Messi] is a good person, but his statements were unfortunate and we Brazilian players did not like that.
"We lost in the World Cup against Belgium and there were also refereeing errors in his favor with Barcelona. I did not hear him talk about corruption at that time."
Peru coach Ricardo Gareca also weighed in on Messi's outburst following the defeat to Brazil.
"Messi is an authoritative voice, that does not mean I agree with him," Gareca said. "I respect him a lot - not just the player but the person. He seems to be very focused.
"But apart from the opinion we have of Messi, we can agree or disagree with him.
"I like that we would know what we have to improve in South America, but that does not necessarily mean that there is corruption or that we are corrupt.
"There is more and more information from Europe, where our children and grandchildren know more and more European players, and it seems that we want to imitate them in everything.
"There are good things in Europe, but we also have good things in South American football, too. I would like to defend South American football.
"If you speak of corruption, you must have convincing evidence. Football is a game and an individual can go wrong."