The Golden Eaglets became just the second side to retain the title depite an early setback.
Nigeria had a golden opportunity to take an early lead, after Chato handled the ball inside the box in the third minute.
Osinachi Ebere took the resulting penalty but his low effort was parried by Mali keeper Samuel Diarra, before the penalty taker saw his follow-up header rebound off the crossbar and a third bite of the cherry was blocked by the Malian defence.
After a goalles first-half, Osimhen broke the deadlock in the 56th minute, finishing with aplomb to set a new mark for the most goal in a FIFA U-17 World Cup tournament.
After conceding the first goal, Mali went further behind when Nigeria made it two goals in three minutes when Funsho Bamgboye got in behind and smashed the ball home to ensure victory for his side.
In the play-off for third, 10-men Belgium accounted for Mexico 3-2 courtesy of a stoppage-time winner.
Dennis Van Vaerenbergh opened the scoring for the Belgians before a Ricardo Marin penalty levelled matters moments later with Dante Vanzeir’s wonderful chip cancelled out by Francisco Venegas’s late leveller. Vanzeir then kept his cool in stoppage time to seal third place.