Africa is a large continent. In a movie African pygmies used blowguns against Europeans. Pygmys never used blowguns. Are there other societies that could have had or still have the blowgun in use. It could anytime in African history. Ancient or pre-colonial, Colonial and even today. Even if the society in question gained it form some other source.
The only definite traditional African uses of blowguns I know of are:
Medieval Egypt, where they were used for hunting birds (with pellets, rather than darts). Egypt and North Africa are the likely path for the introduction of the blowgun into Europe, where it appears in art in the 14th and 15th centuries. Notably, the French and Italian words for the blowgun, sarbacane and cerbottana respectively, derive from the Arabic zabatana, which in turn probably come from the Malay sumpitan (Jett, 1970).
Madagascar, where the SE Asian-style blowgun (presumably brought by settlers from SE Asia) was used for hunting.
It appears to have had no significant use in mainland sub-Saharan Africa. Jett (1991) reports that
there is a tradition among the Wangaturu of Tanzania's interior Central Province, among whom a length of tree with its pith bored out is said to have been used to blow strongly soporific "dust" at victims, to facilitate undetected thievery. A number of other points strongly suggest a Turu connection with Indonesia or Madagascar
References:
Jett, S. (1970). The Development and Distribution of the Blowgun. Annals of the Association of American Geographers, 60(4), 662-688. http://www.jstor.org/stable/2561576
Jett, S. (1991). Further Information on the Geography of the Blowgun and Its Implications for Early Transoceanic Contacts. Annals of the Association of American Geographers, 81(1), 89-102. http://www.jstor.org/stable/2563673
Also see James Stuart Koch, "A Brief History Of Primitive & Traditional Blowguns", http://www.alcheminc.com/blowgunhist.html for a nice Medieval European illustration of blowgun hunting.