After the game finished goalless following extra time, Bruno Alves sent Portugal's fourth spot-kick against the bar and Spain substitute Cesc Fabregas stepped up to sweep Spain into the final at their Iberian rivals' expense.
The sequence of events meant that Portugal captain Cristiano Ronaldo did not even have an opportunity to take a penalty, but Bento said he did not regret electing to put the Real Madrid star in the fifth penalty-taker slot.
"We had defined this plan," he said in his post-game press conference.
"If it had been 4-4 and he had taken the last penalty, we'd be talking in a different way. It's about strategy and we'd defined that before.
"We didn't succeed, but I don't regret anything. We have to look forward and prepare our players for the World Cup qualifiers.
"All the players were tired after 120 minutes. We practised penalties a lot in training, and then we decided who would take them.
"Spain won, and we haven't reached the final. But we're proud to have played like this."
Portugal succeeded in frustrating Spain for long periods of the game but Bento said the second-half introductions of substitutes Fabregas, Jesus Navas and Pedro Rodriguez allowed the Spanish to "exert more control".
"I think we were better in the first 90 minutes," he said.
"Then in extra time, we were less efficient. We couldn't find a goal and when we didn't take our chances, Spain grew stronger.
"We let them play in our half of the pitch in extra time but in the first 90 minutes, we could have decided the game because we were very good in the first half and at the end of the second half.
"We have not lost because of any external factors in this game. We lost because Spain were more efficient with their penalties.
"I don't like to talk about luck too much, but we didn't have any luck during the tournament and I hope that one day we'll have more luck."
Having seen his team emerge from a fiendish group before beating the Czech Republic in the quarter-finals, Bento said his players could take great satisfaction from their performances in Poland and Ukraine.
"We had a very good tournament, if you look at the way that we played and the teams we played against -- Germany, the Netherlands, Denmark, the Czech Republic," he said.
"We now know that we can compete with any team at any tournament."