The Premier League outfit went into Tuesday's Champions League encounter looking to record their third successive win in the competition.
Despite making four alterations and seeing Bologna threaten during the first half, Villa were able to come through with another three points and a clean sheet.
John McGinn's free kick from out wide evaded everyone to put Villa into a lead in the 56th minute before Duran continued his incredible goalscoring exploits during 2024-25.
Morgan Rogers' clever pass from the right was perfect for the Colombia international to help the ball into the far bottom corner from close range.
"He did very good work"
Although he scored his seventh goal of the season, Duran was making just his second start of the campaign having played backup to Ollie Watkins for the past two months.
In the immediate aftermath of doubling Villa's lead, the 20-year-old was replaced by Watkins, leading to an angry reaction once he had made his way back into the dugout.
Nevertheless, Emery chose not to criticise the club's star man of the campaign, acknowledging that it was merely frustration over "wanting more".
Speaking to TNT Sports, the Spaniard said: "They are working well. The commitment to help the team with quality and trying to understand as well.
"He [Duran] scored the goal and it was fantastic and he was wanting more because he was thinking he could score more goals. He did very good work and the last minutes is for Watkins and keep going."
What does win mean for Villa?
Ahead of Wednesday's fixtures when four teams are defending 100% records, Villa are the only team to record wins from their opening three matches.
Realistically, Emery's side only need to avoid defeat in one of their remaining five matches to guarantee a top-24 spot, but they will be firmly focused on finishing inside the top eight which would earn them a place in the last 16.
Next up in Europe is a trip to a Club Brugge side who have three points on the board, a narrow win at Sturm Graz sandwiched between defeats against Borussia Dortmund and AC Milan.