The two sides had tied 2-2 at extra time forcing the winner to be decided through spot kicks.
Kenyan custodian Patrick Matasi was the hero of the game after he blocked three penalties to hand the Harambee Stars their 13th title in the regional tournament at the Kenyatta Stadium, Machakos, on Sunday.
"This was team work as our coach had given us the morale. My coach told me (before the penalties) to concentrate with the ball and not jump around," Matasi said after the match.
Harambee Stars' goals during normal and extra time were scored by Ovella Ochieng and Musa Mohammed while Zanzibar pulled level through a Khamis Musa double.
The Stars will pocket Sh11.5 million in prize money and bonuses including Sh5 million given by Deputy President William Ruto who was in attendance during the match.
Kenya last won the trophy in 2013 after edging out Sudan 2-0 in Nairobi.
President Uhuru Kenyatta congratulated the national team for winning the tournament.
He commended the players and football officials for their teamwork, discipline, determination and vision that yielded the success.
“On behalf of an adoring and grateful nation and my government, I congratulate our national team, Harambee Stars, for playing valiantly right from the preliminaries to the finals and emerging the CECAFA champions. Hongera, you have done us proud,” the President said.
The Head of State said Harambee Star’s victory proved that with proper focus, commitment and organization, the country has the potential to become a soccer powerhouse in the region as well as in the continent.
He affirmed his commitment to supporting the development of sports as an avenue to nurture talents and empower the youth.
-The Star| Nabiswa Emmanuel