With the hosts 1-0 up through a goal from Aguero's Manchester City team-mate Gabriel Jesus, the Argentine looked to be tripped by Dani Alves inside the Brazil box in the 70th minute.
Referee Roddy Zambrano waved away the Albiceleste's appeals for a penalty, with Brazil able to launch an attack of their own which ended in Roberto Firmino making it 2-0 and all but ending the tie.
Despite the presence of VAR the decision not to award the penalty for Argentina was not officially reviewed - a call Argentina captain Lionel Messi blasted as "bullsh*t" in an angry post-match interview.
And Aguero concurred with his team-mate, believing that the blatancy of the foul on him meant some of his team-mates switched off in the build-up to Firmino's goal.
"The feeling is not good. The second goal was controversial," he told reporters. "Juan [Foyth] stops thinking that the referee was going to stop. VAR worked very well until today - incredible!
"We do not pay attention to those things on the pitch, except for the blow that Dani Alves gives me from behind.
"I do not know why he did not check it. At the time, he [Zambrano] may not see it, and they told us that the VAR would become like a fifth referee."
Defeat means Argentina's wait for a senior trophy at international level goes on, with the South American superpower having failed to win anything other than the Olympics (which is contested predominantly by Under-23 players) since lifting the Copa America trophy in 1993.
Performances have improved throughout the tournament in Brazil, however, and Aguero - a veteran of 94 international caps - believes the future is bright under rookie coach Lionel Scaloni.
He added: "It was all very new. We're leaving with a good feeling. There are team-mates who have not previously had the chance to play in competitions like this, and they did very well.
"They are the future of the national team. Rest assured that this is going to change, and we need to give them confidence."