Cuba continued to struggle in the early stages, with Abdul Ajagun passing up another opportunity to send Nigeria into the lead after 15 minutes.
Nigeria did have the lead moments later, however, when Aminu Umar was on hand to finish from close range. It got worse for Cuba after 22 minutes when Umar met a cross from Ajagun before converting past the opposing goalkeeper.
Yordan Santa Cruz came closest to opening Cuba's tally in the first period, but the striker could only fire wide from outside the box.
Olanrewaju Kayode came close to putting Nigeria three goals ahead in the early stages of the second half, but the attacker's effort moved high and wide of the crossbar.
Nigeria had their third with little over 20 minutes remaining, however, when Ajagun stooped low to head home from inside the box.
The Africans had the chance to make it four in the final five minutes, but Ajagun sent a penalty wide of the post.
Next up for Nigeria is a clash with Korea on Thursday, while Cuba face group favourites Portugal on the same evening.