A long-range Marcel Hernandez goal in the 22nd minute of extra time gave the Cubans a 1-0 victory over the eight-time Caribbean champions.
In a largely cagey encounter, Carlyle Mitchell went close for Trinidad and Tobago in just the sixth minute, hitting the post with a header from a corner.
Cuba could have taken the lead in the 61st minute but Jaine Colome Valencia blasted a penalty over the crossbar.
But the extra-time winner gave Cuba revenge for their 2-1 loss to the Soca Warriors in the 1999 final.
As well as crowning the champion of the Caribbean, the tournament also served as a qualifying for the CONCACAF Gold Cup in 2013 which also features teams from Central and North America.
Beaten semi-finalist Haiti and Martinique also qualified for the tournament to be held in the US in July.