Coach Vicente del Bosque admitted Spain were far from at their best as they booked a first-ever place in the World Cup semi-finals.
The European champions reached the last four after a 1-0 victory over Paraguay in Johannesburg on Saturday evening.
A game of two missed penalties and a solitary effort from the sharp-shooting David Villa brought life to an otherwise drab contest.
Oscar Cardozo missed a second-half penalty for the South Americans and Xabi Alonso followed suit for Spain before Villa's decisive strike in the 83rd minute at Ellis Park.
Spain will now face an impressive Germany side in Wednesday's second semi-final.
"In my time a Spanish side never felt so uncomfortable or passed the ball so inaccurately," explained del Bosque.
"But now it's an absolutely marvellous moment for Spanish football and our game is at the very top.
"We didn't play a terribly good match today but we are happy and we know we have the necessary resources to face any rival including Germany.
"It's a great moment for Spanish football. We beat Germany in the final of the Euros but they are among the elite teams and I think that speaks volumes for European football."