The 41-year-old last worked in the Championship in England with Bristol City, before being sacked in January this year after he was unable to guide the club away from the relegation zone.
However, with Aberdeen sat in ninth in the SPL table and with two games of Brown's reign left, McInnes will have to wait until next month's split before taking over the reins and joining assistant manager Tony Docherty at Pittodrie.
A delighted 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 and I can assure, fans, players, sponsors and everyone associated with Aberdeen Football Club that I will do everything within my power to build a team that will entertain the fans and more importantly bring long-awaited success back to this great club.
"First and foremost, we still have a chance to make the top six and while Tony and I do not officially take charge for a couple of weeks, there remains plenty for us to get on with in the interim."
Dons chairman Stewart Milne believes McInnes will be able to build on the excellent work done by Brown and his team between now and the end of the campaign.
He added: "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."