The 40-year-old stated that Atletico were the better side in the two-legged tie and urged the players to lift themselves up for the remaining La Liga matches
Los Che had to overcome a 4-2 deficit from the first leg to go through in the competition, but Adrian's goal in the second half secured Los Rojiblancos a 1-0 victory and a place in the final in Bucharest.
"They were better and deserved to win," Emery told reporters after the game. "It was key for us to score a goal and we were not able to do this.
"We were close to scoring in the first half, but that was not enough. If we had scored, we would have taken the match to our side, but that was not the case.
"I am happy with the fact that we were all together, fans and team, but the first leg played a key role."
Emery also urged his players to switch their focus to what is left to play in La Liga, as Valencia are chasing a top-three finish which will allow them to enter the Champions League next season.
"The most important thing now is that Valencia can compete at the highest level in Europe again and for that, La Liga is the way," he said.
"We are sad that we will not play any final, neither in the Copa del Rey, nor in the Europa League, but now we have to focus on our main goal, which is to qualify for the Champions League."
Spanish sources have suggested that Emery will step down at the end of the season, but the 40-year-old refused to address his future.
"That is not important," he said. "Now it is not the time to talk about my continuity."
Valencia will visit rivals Malaga on Sunday in their next La Liga fixture.