The Super Eagles had to work hard for the victory against the Palancas Negras side that had exceeded expectations in reaching the last eight.
Nigeria dominated the early exchanges with Napoli striker Victor Osimhen denied by the crossbar from Ademola Lookman's pinpoint cross.
But on the stroke of half-time, Moses Simon turned provider, slipping in Lookman who slotted calmly beyond goalkeeper Guilherme da Costa to give Nigeria the lead.
Angola almost equalised soon after the break when substitute Abrosini Salvador was sent through one-on-one but could only rattle the post with his effort.