Oluwakemi Adegbuyi opened the scoring for the Flamingos in the 25th minute.
Puerto Rico fought hard to get back into the game, but the Nigerian girls stood firm at the back.
Defending champions DPR Korea, who thrashed Poland 6-1 earlier in the day, top the standings with six points.
The Flamingos will face DPR Korea in their final group game on Friday.
