The Iberians won their final Group G game, with Cristiano Ronaldo scoring a late winner after Asamoah Gyan had cancelled out a John Boye own goal, but a 2-1 victory was not enough to secure passage to the last 16.
Bento expressed his disappointment at his side's inability to progress and put the blame on his players being too heavily affected by losing 4-0 to the Germans.
"The only thing that can be said is that, in the end, it was a bad result," the 45-year-old told journalists after game.
"We couldn't reach our goal. I think that, after those three games, we got what we deserved.
"The two teams that qualified [for the round of 16] deserved it. I believe we were too affected by the result of the first match, it left a scar on the team."
Portugal ended their campaign level on points with the United States in Group G but went out courtesy of an inferior goal difference, despite overcoming the Black Stars.
"The second part of the game today, we weren't so good but I don't think Ghana caused us too much trouble in the first half," he continued.
"We could've had a bigger advantage. But even after the draw, we had chances of having a bigger score. In the end, all we can do now is evaluate what we did wrong and congratulate Germany and the United States."