The Premier League outfit went into the second leg against Olympiacos facing a 4-2 deficit on aggregate, putting the onus on needing to make a fast start in Greece.
However, Ayoub El Kaabi - Villa's nemesis in the first leg - scored in the 10th minute to leave the West Midlands outfit facing even more of an uphill task.
While Villa had their opportunities, they never looked like getting back into the contest and El Kaabi would score his fifth goal of the tie 12 minutes from time to wrap up a 2-0 win.
As a result, Emery used the final stages to hand game time to some of the club's youngsters, resting key players for the challenges in the Premier League to come over the next 10 days.
What did Emery have to say?
Although Villa have gone through the season as the tournament favourites, Emery is eager for his squad to quickly forget about the experience that they have had on the continent in the hope of finishing the campaign on a high.
Villa finish the season with matches against Liverpool and Crystal Palace as they bid to secure a first-ever appearance in the Champions League.
Speaking to TNT Sports, Emery said: "Firstly get back to Birmingham. Then tomorrow rest and Saturday we focus on the match on Sunday against Liverpool. We are motivated and excited for it. Yes today we are disappointed but only one team can win, so for us to continue with the frustration doesn't make sense.
"My message is clear. Move on and we have to try and finish the season doing an amazing season, particularly if we manage to achieve the last objective. Even without it [Champions League] we are in Europe in the Europa League.
"We will go over what we have done in the last two legs against Olympiakos and try to learn and take positives from it, take the information from it. Take the experience. Recover, reset and move on."
What do Villa need to do in their final two matches?
Theoretically, much depends on the results and performances of Tottenham Hotspur, who trail Villa by seven points but possess a game in hand.
If Villa are to be denied a place at European football's top table, Spurs cannot lose any of their matches against Burnley, Manchester City and Sheffield United.
Spurs' trip to Burnley takes place two days prior to Villa playing host to Liverpool on Monday night, meaning that Emery's men will know if they still need to get points on the board.
Should Spurs beat Burnley, Villa would need to beat Liverpool to be confirmed as a Champions League qualifier. A draw would leave Villa requiring a point, while a defeat at Turf Moor for Spurs would ensure that Villa get over the line without kicking a ball.