The Spanish outfit looked good for a result at the BayArena after taking the lead through Jonas in the 24th minute.
But Leverkusen scored twice in the space of five second-half minutes to come from behind and claim a victory.
Speaking after the match, Emery expressed his disappointment in the result, but not his side's performance.
"I don't see the result as a fair one. We deserved to win and for that reason I am happy with our game but very upset with the result. In the overall scheme of things Valencia were the better side and lost. We knew that they would come at us because they have good players," he was quoted as saying in UEFA.com.
"We also knew they would have their chances and they took advantage of them. We didn't manage to do that during our moments in the game.
"It feels somehow unjust to lose but we have to accept it. We didn't manage to contain them in the opening quarter of the second half but that was also to do with their strength. In the first 30 minutes we were really on top and I was feeling confident."
The defeat leaves Valencia third-place in Group E with just two points.
And Emery knows his side now face an uphill task to progress into the knock-out stages.
He added: "The difficulty in advancing from the group has increased but we must remain optimistic and grab the chances that come our way. Looking at how we played tonight I am optimistic.
"If I didn't believe that Valencia were capable of winning the three remaining games in this group I wouldn't be here. We also know that we're not depending on ourselves now."
Valencia host Leverkusen next on November 1 at the Mestalla.