Despite their dominance throughout, the world and European champions were restricted to just shots from range for the most part and only found a way through a packed Finnish defence when Sergio Ramos headed home from a corner four minutes into the second-half.
However, Spain were stunned 12 minutes from time when Teemu Pukki poked home Kasper Hamalainen's cross from close range to seal a famous night for the visitors.
"I think we failed to finish off the game with the second goal," said Del Bosque.
"They defended well and then the unthinkable happened and they scored a goal.
"We could have been more clinical in front of goal but to not have won is too big a punishment."
Spain will now almost certainly have to win away to France on Tuesday if they are to avoid having to qualify for next year's FIFA World Cup via the play-offs.
David Silva and the Jordi Alba will also be unavailable for the trip to Paris through suspension and injury respectively.
However, Del Bosque remains confident his troops are still capable of automatic qualification even though they trail France by two points in Group I.
"We continue to rely on ourselves. We have a great team and winning in France is possible," he insisted.
"There are four games left and there is still a long way to go."
Finland manager Mixu Paatelainen meanwhile was understandably delighted with the effort and organisation of his side.
"I want to thank our players who were brilliant tonight and remained very organised," he said.
"It was a wonderful night. Spain are the best team in the world and they certainly play a type of football that I admire."
And the former Kilmarnock boss dismissed suggestions his side's set-up had been overly negative.
"The way we played was the best way we thought to get a result and it is that way in every game that Spain play," he explained.
"We had watched videos of other teams playing them and Barcelona and we knew we wanted to hit on the counter-attack."