The former St Johnstone and Bristol City boss and regular assistant Tony Docherty have signed two-and-a-half-year deals and will take up their posts after next month's SPL split.
And that means Craig Brown has just two games left of a managerial career which began in 1977.
Craig Levein and Ross County manager Derek Adams were also linked with the job, but Aberdeen chairman Stewart Milne said McInnes and Docherty "ticked all the right boxes".
"From the moment Craig Brown announced his intention to step down, Derek and Tony were at the forefront of our thoughts alongside other potential candidates," Milne said.
"We were all hugely impressed with Derek's assessment of the club, its potential, and what they believed was required to move it on from the strong platform that Craig and Archie Knox have established."
McInnes said: "I'm absolutely thrilled to be given the opportunity to manage a club of the stature of Aberdeen Football Club and I'm determined to repay the faith the Pittodrie board has shown in me.
"Having been given an outline of the club's vision of the future I can clearly see the ambition here."
Brown is staying at Pittodrie in a director's role, and Milne said: "I would again like to extend our appreciation to Craig and Archie for their contribution to Aberdeen Football Club."