Papua New Guinea's not in Africa (but still intriguing idea.)  
 
 
I can't claim to be an expert, but 
Shangaan Electro's been discussed here before. And it's not quite EDM, but check out 
Konono Nº1...
Konono Nº1 is a 
Grammy nominated musical group from 
Kinshasa, 
Democratic Republic of the Congo. They combine three 
electric likembé (a traditional instrument similar to the 
mbira) with voices, dancers, and percussion instruments that are made out of items salvaged from a junkyard. The group's amplification equipment is equally rudimentary, including a microphone carved out of wood fitted with a magnet from an automobile 
alternator and a gigantic horn-shaped amplifier. The group achieved international renown beginning in 2005, with its 
DIY aesthetic appealing to many fans of 
rock and 
electronic music. They played this same year at the 
Eurockéennes festival in France.
 
The sound they make is RAW AS FUCK.
You can find threads here about Kwaito, which I honestly know next to nothing about (South African house-derived style)
Then on the more melodic tip there's Tinarawen, a Tuareg group that's into traditional north African music and Bob Dylan...  
 
 
And then going back in time there's SO much - I can't recommend the Ethiopiques series strongly enough, especially the stuff coming out of Addis Ababa in the seventies: really fast full bore orchestral funk with totally foreign musical modalities, like James Brown got together with a bunch of fucking Martians (to western ears.) Volume 8 is my favorite, "Swinging Addis." Instant party music.
King Sunny Adé is interesting too. In fact, a lot of West African Hi-Life music is really good, very danceable with lots of catchy melodies.
Then in traditional music I like the drummers of Burundi (true fact: their sound was ripped off by Malcolm McLaren to create the template for the Adam & the Ant/Bow Wow Wow sound of the eighties). It's kind of hard to go wrong with any archival recordings of traditional percussion material; if you make music, you will come away influenced...