Fulham had Joachim Andersen sent off, with Jaden Philogene also seeing red for Villa. The visitors won via goals from Morgan Rogers, Ollie Watkins and Issa Diop, who put through his own net. Raul Jimenez had initially put Fulham ahead on five minutes.
“I’m very happy for the supporters that travelled here with us,” Emery said.
“Now we’re going to prepare for the Champions League and we’re enjoying the Champions League because last year we performed perfectly in the Premier League being very consistent.
“We were very focused in our demands to get Europe and achieving Champions League and we are enjoying it, but today the Premier League was most important for us.
“The supporters are aware of how important the Premier League is for us to play again in Europe next year, hopefully in the Champions League.
“Today I focused with the players on those three points, respecting the opponent and doing our game plan as strong as possible to get the performance we wanted and the win.”
Villa goalkeeper Emi Martinez also denied Andreas Pereira from the penalty spot.
Emery added: “Emiliano is fantastic and we needed the goalkeeper before, we needed him today and we will need him again.
“We have the best goalkeeper in the world, Emiliano Martínez. It means matches like today and moments like today with the penalty to be there to save us.”