The boss initially thought Spanish referee Gil Manzano had awarded his team a goal when Morgan Rogers swept home from close range after visiting keeper Michele Di Gregorio spilled a free-kick deep in stoppage time.
But the effort was chalked off, amid some confusion, with Diego Carlos adjudged to have fouled Di Gregorio as he went for the ball.
Emery thought the goal would likely have stood in a Premier League match.
He said: “With the last action, it is the interpretation of the referee. In England, 80 per cent of those is given a goal and it not a foul. It's very soft.
"But in Europe, it could be a foul. We have to accept."
Rogers and several other Villa players ran to celebrate, as it was not immediately clear whether Manzano had awarded a goal or a free-kick.
The referee eventually ruled out after Di Gregorio had received treatment. Emery suggested the referee had
Emery continued: “Everybody will know, in England the interpretation is different.
“The England referees, when actions like that the interpretation is a clear no foul but in Europe that interpretation is different.
“They have to be working to get the same decision when some action like that is coming, maybe yes, I don’t know exactly why but we knew before in the Premier League that it is different.
“In Europe for example we are not doing block like in England and we are not doing in front of the goalkeeper in offensive corners the same situations like in England.
“When the action happened, I was thinking here in Europe it’s a foul. In England not, but in Europe I have to accept it.
“At first, I thought the referee gave us a goal. In cases like that, it's confusing because he has to wait for VAR. I don't know what happened but I think so (the referee changed his mind with VAR)."
Despite the late drama, Emery expressed satisfaction with his team’s performance and a point which leaves them ninth in the Champions League group stage table.
“We were closer than them to winning the match,” he said. “They're very difficult to beat but we created a plan. There weren't many clear chances for either team.
"It was a tight match for both teams but I am happy with the overall picture in the Champions League. We still have the possibility of finishing in the top eight."