The incident happened before kick-off when fans tried to get entry to the Makhulong Stadium in Tembisa, east of Johannesburg.
The match got under way on time with Nigeria running out convincing winners in their final fixture before the main event starts on Friday.
Everton striker Aiyegbeni Yakubu opened the scoring after 17 minutes, finishing off a swift move with a crisp finish.
Victor Obinna made it 2-0 from the penalty spot 15 minutes into the second half only for Jong Tea-se to pull one back after a mistake from Elderson Echiejile.
Obafemi Martins sealed the win – a first under new coach Lars Lagerback – with Nigeria’s third following good work from Kalu Uche.
A disappointing afternoon for North Korea was compounded when Cha Jong-hyok was sent off after picking up two yellow cards.