Winners were selected by fans sending text messages, said Alison Reid, a spokeswoman for MTV Networks Africa.
Africa has long featured a vibrant music scene, but artists have had difficulties breaking into overseas markets. Famous African artists include Senegal's Youssou N'dour, Nigerian legend Fela Kuti and South African impresario Miriam Makeba, who died this month.
MTV hopes the awards can offer the artists more exposure and celebrate the continent's artistry.
Performers from South Africa, Kenya, Ghana, Gabon and others also were nominated. Songs by D'banj and Naeto C, both male, are all but ubiquitous on the radio in Nigeria, Africa's most-populous nation of 140 million people.
African music is highly varied, reflecting myriad tastes in the vast continent. Included across the many genres are call-and-response chanting and heavy drumming, drawing on pre-colonial modes of communication among villages.
Since independence movements swept the continent in the 1960s, African music also has increasingly been open to outside influence, incorporating salsa rhythms, rock beats and, increasingly, hip hop and R&B styles.
Many of the new Nigerian acts nominated Saturday feature heavy beats pioneered by American rappers and hip-hop artists. The lyrics often reflect the desire of many Nigerians to escape poverty and corrupt governance.
MTV's regional music channel MTV Base now reaches almost 50 million African viewers in 48 countries through a network of pay-per-view services and partnerships with domestic channels.