Watkins, who scored 108 goals in 278 appearances for the Villans in all competitions, is set to join Al Hilal in the Saudi Pro League after refusing to play in the 4-0 defeat at Brighton last week.
Earlier this week, Villa agreed a deal worth a total package of £65 million to sign striker Nicolas Jackson from Chelsea in what is a swift replacement for Watkins before the summer window slams shut.
Speaking in his latest press conference, Emery revealed that Watkins will be replaced as he waved the striker farewell.
"I can tell you now Watkins, his commitment and his behaviour was fantastic," said Emery.
"We didn't get a deal to finish his last match playing at Brighton, but he told us after the match he was sorry and he told us as well he made a mistake.
"He was wrong, but we accepted it. The players as well because he always had very good behaviour and commitment with the club, with us and with me.
"For me, it's a fantastic guy, a fantastic guy even more than a player. I told him bye with a huge hug and with small tears.
"But now it's a new chapter here with Nicolas Jackson and we replace him."
On replacing Watkins: "In football if you are expecting transition, maybe you are not in the right way. We have to rebuild the team as fast as possible. We have to accept our way, our decisions and why we are taking some decisions."
With Tammy Abraham injured and missing the start of the season, there is a chance that Villa aim to sign another forward before the window closes in less than a weeks time.