The host will play second finisher of Group B Chile on June 28 in knockout stage.
Neymar opened the scoring in the 17th minute but Joel Matip equalized the match in the 26th minute.
Neymar was on target once again in the 35th minute. Fred and Fernandinho scored in the 49th and 84th minutes to ensure the Brazilian team finish on top of Group A.
"We improved again from the Mexico game. We can still get better, and we know that Chile are a very good side,” Brazil coach Luiz Felipe Scolari said in the post match news conference.
"They have a lot of quality. If I could choose, I would choose another opponent. South American sides are always tough," he added.