Spain's all-time top goalscorer netted the first goal before coming off before the hour in their 3-0 win over the Socceroos to end their dismal World Cup campaign on a high.
Villa was visibly emotional as he sat on the bench throughout most of the second half and the coach says he understands the former Barcelona star's disappointment, but didn't realise it was his final game.
"I'm sure he was angry," he told reporters. "He says it was his last game and I didn't know. I'm sure he was disgusted. It was the moment to close the game out and we did so."
Despite having guided Spain to a World Cup win four years ago and the retention of their European Championship crown, Vicente del Bosque's future is in doubt as his side lost to Netherlands and Chile to crash out at the group stage. But Del Bosque insists Spain have a bright future, no matter who is in charge, adding that a decision on his own future will be made soon.
"In the last six years we've been number one in the world. It is a group of players that have learnt a lot, they've played well but now we're out," he said.
"We have to move forward and qualify for the next tournament, and whoever the manager is, the future is safe.
"The president secretary and I will speak and we'll look for the best solution possible for Spanish football in the next few days or next week. There's no rush."
Del Bosque was happy with Monday's win but said his team didn't play well enough in the previous two games.
"We've finished off in a dignified manner, the players gave their all. You have to think we've been a bit below par and that Netherlands and Chile played well, and were very strong."