Brazil ran out 2-0 winners in Belo Horizonte on Tuesday despite Argentina recording 14 shots to the tournament hosts' four.
Aguero hit the crossbar with a header and Argentina captain Lionel Messi later struck the post, while Lionel Scaloni's side twice saw penalty appeals rejected.
Messi described decisions that went against his team as "bulls***" in the aftermath and Aguero, who appeared to be fouled by Dani Alves in the box, was similarly disparaging over the performance of referee Roddy Zambrano and his colleagues.
"The feeling is not good. The second goal was controversial," Aguero 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 [the referee] did not check it. At the time, he may not see it, and they told us that the VAR would become like a fifth referee."
There were contrasting emotions for Aguero's Manchester City team-mate Gabriel Jesus, who scored the opening goal and then superbly set up Roberto Firmino to clinch Brazil's first Copa final appearance since 2007.
"I'm speechless. I consider every match to be important, even the ones I don't perform well, because I take lessons from them," said Jesus, who struck his first goal of the tournament.
"Tonight I decided I was going to score, I was very confident from the kick-off. I missed a chance, then I managed to score. Firmino was able to spot me well, it gave me confidence.
"I'm very happy not only for the goal, but for how the team performed. Last week I've said they would struggle to break our defence. We worked hard and battled hard tonight.
"Unfortunately we couldn't score against Paraguay but we grabbed the goals tonight. Everyone should be pleased for the match they played, for the effort.
"This is Brazil! We have to play every match as we've been playing, with the same spirit, that we will achieve our goals."
Brazil, who have kept clean sheets in all five of their matches, will play either Peru or defending champions Chile in Sunday's final.