The Flying Eagles made a lively start and could have taken the lead when Odion Ighalo mis-hit the ball with just the goalkeeper to beat from five yards. King Osanga also fire in a right-footed shot from 25 yards that forced Sergio Asenjo into a scampering low save.
However, as the game wore on, Spain began to move into the ascendancy. Emilio Nsue chested the ball into the path of Merida, who hit a left-footed volley which flew just over the bar. Uche Okafor then turned away a shot from Nsue, but in the 33rd minute the Europeans' pressure paid off.
Playing the offside trap, Nigeria failed to catch a late, well-timed run from deep from Merida, leaving the Arsenal man in acres of space, before he produced an extremely composed finish to lob the ball over the onrushing Okafor. Merida also had a great chance to double his team's advantage on the stroke of half-time, but saw a low shot brilliantly saved by the Nigerian keeper.
Neutrals were left to assume that Siasia had a few harsh words to say to his players at half-time and that his opposing coach Luis Milla ordered his players to protect their lead, given the balance of play in the second half. Spain sat back deep, inviting a lot of pressure from Nigeria, which almost cost them their lead.
Half-time substitute Omatsone Aluko forced a brilliant save out of Asenjo and in the 67th minute, Daniel Adejo headed the ball into the net, but his effort was ruled out for an infringement in the box before the corner was taken. Rabiu Ibrahim and Gbolahan Salami were both wayward in their finishing when well placed and, completely against the run of play, Spain added a second.
Ibrahim was adjudged to have tripped Ander Herrera in the box during a rare Spanish attack and Merida chipped home the resulting penalty in the 83rd minute. Just 60 seconds later, Salami was red carded for striking out at the double scorer to cap a truly miserable afternoon for the Africans.
The result leaves Spain battling it out for Venezuela for top spot in the group, with qualification likely to be secured by the end of the day unless Tahiti can spring a surprise against the Venezuelans. Nigeria, meanwhile, must look for a big win over Tahiti and hope results elsewhere go their way if they are to remain in the tournament.