After a strong start from the hosts, the away side took control of the contest with two goals in ten minutes.
Enzo Fernandez curled in a free-kick nine minutes after the restart to extend the lead, with Moussa Diaby responding in stoppage time.
“I’m disappointed we didn’t get a good result,” Emery said.
“We did good effort and got a good result in Chelsea, so we were very excited and motivated for the match tonight here with our supporters.
Aston villa manager is not happy with the results
“We started very well and were creating chances, being close to score. They created chances and they were more clinical than us.
“In the second half we didn’t start like the first half and found it difficult to create clear chances.
They scored the one chance they had with their set piece.
“At 3-0, it was very difficult but our spirit was good and we reacted by creating chances. We were pushing with our supporters here to get a goal and have options to get the result back.
“We scored so late and didn’t have time to get more.”
After exiting the cup, Villa turn their attentions back to the Premier League.
Another home game against Manchester United awaits on Sunday, and Emery is keen to continue their strong form in the top flight.
He said: “We are trying to separate each competition and we are being consistent in the Premier League.
“We lost the last game here at home but we reacted very well in Sheffield
And we’re going to try again on Sunday here against Manchester United.
“We will try to get positive energy and a good performance in our collective tactical way.
“Team will again be focused on the league because in the league we’re feeling strong.”