Blind has put pen to paper on a four-year contract at the Johan Cruyff Arena, returning to the club where he began his career and spent six years before joining United.
The 28-year-old fell out of favour with Mourinho last season, making just four Premier League starts, but the United boss was still full of praise for the Dutchman following his departure.
"I would like to say a big thank you to Daley Blind for everything he has done for the club since he joined in 2014," Mourinho told the club's official website.
"I have to say, that in my 18 years of management, Daley is the one of the most professional players, both on and off the pitch, that I have had the pleasure to work with.
"I would like to take this opportunity to wish him all the very best as he rejoins his boyhood club, Ajax, and thank him for from the bottom of my heart for his commitment and dedication over the past two seasons."
Blind made 141 appearances for United, helping the club to FA Cup, EFL Cup and Europa League glory.