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Bristol City midfielder Tommy Doherty, making his home debut, saw a clever 22-yard curler palmed away for a corner by keeper Iker Casillas after eight minutes.
At the final whistle, Northern Ireland were applauded off the pitch by their appreciative supporters.
It was a proud night for Aaron Hughes, who had captained Northern Ireland for the first time in a 0-5 defeat at home to Spain in April 2002.
This time the skipper wore his Newcastle number, 18, hoping it would bring him better luck in international football, and the home side certainly had fortune smile on them as they clung on for a good point.
The result leaves Spain in second place in Group Six, one point behind Greece.
Northern Ireland are bottom, having picked up just their second point of the campaign.
Northern Ireland: Taylor, Baird, McCartney, Aaron Hughes, Kennedy, Griffin, Johnson, Doherty, Jones, Healy, Andrew Smith.
Subs: Carroll, Williams, Toner, McVeigh, McCann, Hamilton, Elliott.
Spain: Casillas, Puyol, Marchena, Helguera, Juanfran, Etxeberria, Baraja, Sergio, Vicente, Valeron, Raul.
Subs: Salgado, Canizares, De Pedro, Morientes, Bravo, Joaquin, Gabri.
Referee: Claus Bo-Larsen (Denmark).
Meanwhile John Acterberg has signed a new two year deal with Tranmere Rovers eliminating any chance he had of signing for the Latics.