On their road to the final, the Crested Cranes humiliated Botswana 12-0, while Bantwana beat Zambia 2-1 in their respective semi-final.
While South Africa was bidding to avoid back-to-back Cosafa youth title misses after the U20 Women lost in August, the East African guests were aiming to emulate Tanzania's U20 success.
After a goalless first half at the Francois Xavier Stadium, Ayub Khalifah's side secured the lead through Fauzia Najjemba thanks to Juliet Nalukenge's assist in the 56th minute.
In the 74th minute, Bantwana got back into the mix when Nabeelah Galant teed up Tiffany Kortjie to score the equaliser.
Despite efforts from Simphiwe Dludlu's side for a late winner, the tournament's leading scorer Nalukenge grabbed her 18th goal of the competition three minutes from time to seal Uganda's victory.
#Uganda 🇺🇬 have been crowned champions of the inaugural 2019 COSAFA Women’s Under-17 Championship after a hard-fought 2-1 victory over #SouthAfrica 🇿🇦 in the final at the St Francois Xavier Stadium in Port Louis, Mauritius on Sunday. https://t.co/wN9BxY1Jgr pic.twitter.com/86e1hbQGaS— COSAFA (@COSAFAMEDIA) September 29, 2019
The result means Uganda are the winners of the maiden Cosafa U17 Women's Championship, while South Africa finished as runners-up.
Zambia beat Botswana 3-0 to win the bronze. For individual honours, Uganda's Nalukenge claimed the topscorer gong, and her compatriot Daphine Nyayenga, who conceded just a goal claimed the golden glove.
South Africa captain Jessica Wade was voted the Player of the Tournament while Botswana won the competition's Fair Play award.
Here is the hall of fame...— COSAFA (@COSAFAMEDIA) September 29, 2019
Player of the tournament : 🇿🇦 Wade
Golden boot : 🇺🇬 Juliet
Golden gloves : 🇺🇬 Nyayenga
Fair play : 🇧🇼 Botswana
🇺🇬 2 - 1 🇿🇦#COSAFAWU17 #Mauritius #COSAFATV, @CAF_Online, @CAF_Media, @SAFA_net, @OfficialFUFA, @FAZFootball, @WeAreBFA