Spain goalkeeper Iker Casillas saved Joao Moutinho's penalty then Bruno Alves hit the bar to open the door for substitute Cesc Fabregas, who scored the decisive kick via the post after a 0-0 draw during normal and extra time.
"We lost because Spain were more efficient in the penalties, but it's true that we did not have any luck in this tournament," Bento told a news conference.
Asked why the world's most expensive player Ronaldo did not step up to take a penalty, Bento said it had been agreed that the captain would come forward for the final spot-kick.
"We had this plan and if it would have been 4-4 and he would taken the last penalty we would be talking in a different way," he said.
The coach found much to praise in Portugal's battle with holders Spain, as well as their displays during the showcase in Ukraine and Poland.
"In my opinion we have played a very good tournament. If you consider how we played today I think we were better in the first 90 minutes, then in extra time we were less efficient," he said.
"If you don't have this little bit of luck then you miss it. We didn't have much luck in this game."
Bento also hailed Portugal's Iberian neighbours.
"Spain really deserve to be in the final, but at the same time I want to thank my players for what they have shown in this tournament," he added.
"I think we played very competitively, we are an aggressive and cohesive team... the way we lost allows us to have a lot of confidence."
Alves had looked set to take the third penalty but Nani suddenly appeared behind him, took it and scored. Alves then came back for the fourth spot-kick but struck the bar, handing the initiative to Fabregas.
"There was some confusion with Bruno Alves and with Nani, then Bruno took the penalty... and it was decisive," the coach continued.
"Penalties could have been an advantage for us, but we lost the advantage after the first one," Bento said, referring to Moutinho's opening miss after Xabi Alonso also failed for Spain.
