Spain came into the match as one of the tournament favourites after dominant wins in their two previous Group C games but departed the Wellington Regional Stadium chastened after being outplayed by the 2011 champions.
"This defeats really hurt," said Vilda, who has been in charge of the national team for eight years.
"This is the worst defeat that the national team has had while I've been the coach. They are also affected by this defeat. It hurts. They are angry."
Vilda congratulated Japan on their performance and conceded that Spain had struggled to break down the Nadeshiko defence despite dominating possession.
"We passed the ball many times, but horizontally and that was not what we were looking for," he added.
"What we always look for is to reach the opponent's goal. Today we were not able to achieve this and we hoped in the next game, the same thing won't happen."
Japan hit La Roja on the break for three first half goals before grabbing the fourth in similar style late in the second.
Vilda, though, said the defensive frailties had not been the full extent of the problem.
"It is quite clear that there was not a good feeling in general," he said.
Already qualified for the knockout stage before the match, the Spanish will now move north to Auckland to take on Switzerland in the last 16 on Saturday.
"I have no doubt whatsoever that my team is going to react, I have no doubt whatsoever that the attitude against Switzerland is going to be different," he added.
"They are very angry. They're going to be very keen, it's the round of 16 of the World Cup. No one should lose hope because we're all very hopeful and my confidence in this team remains."