The 30-year-old striker, who is a product of Arsenal's academy, will join the Dons on a two-year deal once the transfer window opens next month.
Emmanuel-Thomas joins former Scotland captain Scott Brown and Scotland international Declan Gallagher in committing his future to a new era at the Granite City club under Stephen Glass.
The Aberdeen boss told the club's official website: "We're pleased to add Jay to our squad.
"His arrival is a sign of intent and marks the first piece of the jigsaw as we look to re-build our front line.
"He brings a lot of attacking flexibility and can play in numerous positions as we look to add firepower to the group we have here.
"We're working diligently behind the scenes and assessing players who fit the profile we are looking for here at Aberdeen.
"It is imperative we take this opportunity to add the necessary quality of players and I look forward to enhancing our attacking options in the coming weeks."
Emmanuel-Thomas said: "It feels great to be an Aberdeen player.
"Within football, Aberdeen has always had a very good reputation and to be involved with such a big club is a great feeling.
"Based on games I've played against Aberdeen, watching the style of play, what the set-up is like behind the scenes and knowing where the manager wants to take the club, of course it was something I wanted to be part of."