Chile grabbed a consolation, before Funsho Bamgboye saw his marching orders, with Osimhen's late header adding some gloss to the win, despite Nwakali missing his second penalty of the match after Chukwueze had been fouled in the penalty area for a third time.
He then played a big part in the second Nigeria goal, sprinting onto a long upfield clearance and tapping the ball past the sliding Juan Jose Soriano in the penalty area. The Chilean defender’s challenge brought down the Nigeria No8 and Nwakali doubled his side's lead.
Chukwueze then grabbed his second of the game thanks to sheer determination on the hour mark. He worked his way into the Chilean penalty area, performed a couple of stepovers and, after seeing an initial shot blocked, slammed a left-footed strike past Lopez.
Chile's defence will be glad to see the back of the Nigerian No8, as he burst into the Chilean penalty area once more moments later and was felled again, this time by substitute Brian Leiva. For the second spot kick, it was Osimhen who stepped up, and he matched Nwakali's first effort by firing home.
Substitute Funsho Bamgboye later hit the post before Chile's consolation came courtesy of Marcelo Allende, who slammed past Akpan Udoh from Luciano Diaz's cross.
Despite Bamgboye's late dismissal, for a rash challenge, Nigeria rallied and Osimhen grabbed his third of the tournament in two games. Nwakali then missed his chance to double his own tally for the game from the penalty spot, after Chukwueze had been fouled for a third time.
It did not matter though, as Nigeria join Korea Republic in the last 16, with Chile set to face USA in a pivotal final clash back at the Estadio Sausalito on Friday.