The Uyo team will now represent Nigeria in the 2018 CAF Confederation Cup alongside Enyimba.
Akwa, who won the tournament in 2015, grabbed N25m for their efforts while Tornadoes went home with N10m.
Gabriel Okechukwu scored the last kick of the shootout after the regulation time ended goalless.
Akwa started with Ojo Olorunleke, Ottobong Effiong, Kojodvi Dadzie, Afeez Aremu, Godspower Igudia, Emmanuel Ariwachukwu, Ubong Friday, Musa Newman, Christian Pyagbara, Ifeanyi Ifeanyi and Cyril Olisema.
Tornadoes fielded Mustapha Aliko, Reuben Ogbonnaya, Andrew Ikefe, Sunday Akinmoladun, Hussain Isah, Abdulkadir Zango, Musa Wakili, Bolaji Adeyemo, Ibrahim Babawo, Sani Rabiu, and Wilfred Ammeh
Minna club Tornadoes started the brighter of the two sides and got their first chance at goal in the fourth minute when Babawo was through on goal but shot the ball over the bar.
Akwa grew into the game and got their chance in the eighth minute through Ifeanyi, whose effort was cleared by the defenders.
In the second half, Tornadoes sat back while Akwa piled pressure on them. But the Uyo outfit could not find a way through.
In the 86th minute, substitute Okechukwu, who replaced Newman, was through on goal but blazed his effort over the bar with Aliko to beat.
The match went straight into penalties after regulation time and Hussaini and Ogbonnaya converted for Tornadoes while the other kickers lost theirs. Dadzie, Olisema and Okechukwu converted their kicks for Akwa to win the title.
Olorunleke was adjudged the Best Goalkeeper as well as the Most Valuable Player of the competition while Pyagbara was the highest goalscorer.
CAF President, Ahmad Ahmad; Lagos State Governor Akinwunmi Ambode; and Akwa Ibom State Governor Emmanuel Udom watched the final.