The teams had played out a barren draw after extra-time before the Falconets won the ensuing penalty kicks at Boubker Aamar Stadium.
In the semi-final on Monday, Christopher Danjuma's side cruised past Algeria 3-0, while Cameroon required extra-time to subdue hosts Morroco 3-1 on the same day.
Both teams had a fair share of dominance throughout the encounter as the West Africans held sway in the first half, while the Central Africans were outrightly better in the second half.
Favourites Nigeria made a bright start as the Monday Gift led attack caused the Cameroonians a lot of trouble but could not find a breakthrough in the opening 45 minutes.
With Gift replaced 10 minutes after the restart, Charles Kamdem's side forced goalkeeper Chaimaka Nnadozie to make breathtaking saves but couldn't get the breakthrough.
With no goal in regulation time, both sides failed to take their chances in extra time too, dragging the tie into a penalty shootout.
The Falconets bounced back from two misses in three attempts thanks to three consecutive saves from young sensation Nnadozie to claim a 3-2 win.
APK: Cameroon U20W 0-0 Nigeria U20W [2-3 on PK]: The Falconets are champions of African Games through Chaimaka Nnadozie's goalkeeping heroics after a penalty shootout win over the young Lionesses in Rabat.#AfricanGames #Rabat2019 #CAMNGA— Samuel Ahmadu (@sam4wigan) August 29, 2019
The win means Nigeria have won the African Games for the first time since 2007 in Algiers and their third crown in five attempts.