Joseph Mathenge won the top prize for his work "Images of Terror," which first appeared in Kenyan daily newspaper The Standard.
Mathenge's photographs revealed the horrific attack from inside Nairobi's upscale Westgate shopping mall in September 2013.
Mathenge said: "It's a great honor, and I'm humbled to receive this award. All finalists who are here deserve this award. I hope it will motivate men, women and children of good will all over the world to fight terrorism. Memories fade with time, but pictures don't. We felt it necessary to capture each and every moment so that generations to come may see the horror."
The chairwoman of the judging panel, Ferial Haffajee, said: "Joseph Mathenge's photographs so eloquently captured one of Africa's toughest 21st century moments that they were worth a thousand words. That said, the quality of all the winners' works made the contest a tightly run one."
The overall award carried a substantial cash prize, in addition to a three-week CNN Journalism Fellowship at CNN Center in Atlanta. All finalists received a cash prize and an iPad Air, with runners-up receiving an iPad mini.
Mathenge was among a group of 28 finalists from 10 nations who attended the ceremony in Tanzania on Saturday following a four-day program of workshops, media forums, networking and sightseeing.
Deborah Rayner, senior vice president of international newsgathering TV and digital for CNN International, said the awards showcase excellence in journalism in Africa.
"By entering these awards, they have proved they have the determination, professionalism and courage to showcase Africa's stories to the world."
Rayner presented the top accolade to Mathenge alongside Jakaya Kikwete, president of Tanzania, and Nico Meyer, CEO of MultiChoice Africa.
Meyer said: "We are proud to recognize your excellence in journalism and to reward you for your courage in telling stories that would have otherwise remained untold."
Imtiaz Patel, group CEO of MultiChoice South Africa, praised the finalists' role in advancing journalism in Africa. "Your work echoes a great future for the role of the journalists and serves to further strengthen the role of the media in Africa."
Now in their 19th year, the awards were established in 1995 to encourage, promote and recognize excellence in African journalism.