Marisa Garcia gave the Europeans the lead in the 13th minute after finishing a fine move involving Noe Bejarano.
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Nigeria goalkeeper Ineoma Uzoma made several saves to keep the scoreline close, while Folajomi Olabiyi was denied by Laia Lopez after breaking through on goal.
Spain continued to control proceedings and sealed victory in the 73rd minute when Alba Cerrato beat Uzoma with a left-footed effort.
The result leaves Spain second behind China, who defeated New Caledonia 5-0 earlier.
The Falconets will now look to respond when they face China on Thursday, September 10, knowing another defeat could seriously damage their hopes of progressing from Group F.