McInnes and Tony Docherty, his assistant at both St Johnstone and Bristol City, have signed contracts that tie them to Pittodrie until the summer of 2015 with the option of a rolling contract after that.
A club statement read: "Aberdeen Football Club can confirm Derek McInnes and Tony Docherty as their new football management team with the pair set to officially take charge following the SPL split in just under a fortnight's time."
Aberdeen revealed Brown, who was involved in the recruitment process ahead of his official appointment as non-executive director, would remain in charge of team affairs for the next two games along with assistant Archie Knox.
Ninth-placed Aberdeen, who are two points off the top six, host Hearts on Saturday before playing Dundee United at Tannadice in the final match before the split.
Chairman Stewart Milne said: "Craig and Archie also spoke with Derek to establish the most appropriate timing for a handover of duties and all agreed that bringing them in now would enable the incoming management team to have time to familiarise themselves with their new club, while Craig and Archie continue with their preparations over the next two games for a final push towards a top-six SPL position."
McInnes declared himself "absolutely thrilled" to be appointed and assured fans he could clearly see the ambition of the club having been presented with the board's vision of the future.
He added in the club statement: "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.
"In tandem with trying to finish the current campaign in as high a league position as possible, I will also of course be assessing the squad with next season in mind.
"There is so much to do, so many opportunities and I'm really looking forward to get started."
- Sports & Recreation
- Aberdeen Football Club
- Derek McInnes
- Tony Docherty