After a dominant opening period, Desire Oparanozie put the Super Falcons in front after 12 minutes with a superb free kick.
Asisat Oshoala then doubled Nigeria’s lead two minutes from the end of an enthralling first half.
Only twice since the inaugural African Women’s Championship in 1991 have the Nigerians failed to win the trophy. Equatorial Guinea are the only other winners – in 2008 and 2012 – but failed to qualify for this year’s tournament.
Cameroon coach Enoh Ngatchu said reaching the World Cup for the first time in a decade can help transform the game in his country.
Nigeria and Cameroon had already qualified for next year’s World Cup in Canada by reaching the final.
They will be joined there by Ivory Coast who beat South Africa 1-0 in the bronze medal match on Saturday.
In an even contest, also played in Windhoek, Rebecca Ida scored the winning goal six minutes from full time.
She pounced on a loose ball in the Banyana Banyana box from a corner kick, and slotted the ball home.