The hosts ran out 2-0 winners in Belo Horizonte, with Gabriel Jesus and Roberto Firmino scoring.
But the Barcelona superstar was furious that the video assistant referee (VAR) system was not utilised to inform two shouts for a penalty. Three Uruguay goals in their quarter-final exit to Peru were chalked off as well as strikes for Chile in their last eight game with Colombia.
And after yet more heartache with Argentina, Messi did not hold back in his criticism at the way it has been used.
"They were not better than us. They found the net early and the second goal came from a penalty [to Aguero] they didn't award," Messi told reporters
"They [the officials] had called a lot of bulls***, but they didn't even check the VAR, that's unbelievable.
"That happened all over the game. At the first glance of contact, they ruled in their [Brazil's] favour and this kind of bulls**t distracted us from the game
“Throughout the tournament they called bulls*** handballs, bulls*** penalties, and bulls*** fouls. But somehow today, they refused to use VAR.
"There is no excuses for us, but we need to review this, analyse it and let's hope CONMEBOL does something about it - but surely not, because Brazil commands too much power in the organisation.
"I spoke to the referee and he said he would respect us that he would look after us but at no moment did I see that.
"I think we played a great game. We made a great effort and they were not superior to us."
Messi said the referee had shown Argentina no respect: “I spoke to the referee and he said he would respect us that he would look after us but at no moment did I see that.”
Aguero appeared to be tripped by Dani Alves in the second half but no foul was given and Brazil immediately launched a counterattack which saw Roberto Firmino double their advantage.
Argentina defender Juan Foyth was so stunned that a foul was not given that he did not rush back to halt a run by Gabriel Jesus which led to the goal.
Later in the game, defender Nicolas Otamendi went to the ground after tangling with Brazil’s Arthur at a corner, but Argentina’s appeals again proved futile.
With Sergio Aguero also criticising the officials.
“They told us that VAR would be like a fifth referee but when things turn out like this I’d rather it wasn’t there,” said Aguero.
“I was running into the area and Alves stopped me with his foot, it was clear, so clear that Foyth stopped and waited for it to be given.”
Additional reporting from Reuters
Join our commenting forum
Join thought-provoking conversations, follow other Independent readers and see their replies