The 21-year-old Poland forward moved to the BayArena in 2012 but made just a handful of appearances before being loaned out to Augsburg last term and the Dutch champions this season.
He has been in impressive form in Amsterdam - scoring 17 goals in all competitions - and the capital club have brought him in on a four-year deal for a fee believed to be in the region of €2.8 million.
And Milik, who is currently recovering from a knee injury, is looking forward to his future in Netherlands.
"Of course I still feel my knee injury but this is a wonderful day for me," he told the club's official website.
"I see this as a reward for my good work during training and matches and my goals. Basically for everything I've done here.
"We have the goal to work with a young group in the coming years and build something here at Ajax. My aim is to become champions and score lots of goals.
"The next few weeks I will be focused on my recovery. After that I will set me eyes on the future, and that future is with Ajax."