The duo, who worked together at both St Johnstone and Bristol City, have signed until the summer of 2015 with the option of a rolling contract thereafter.
McInnes was seen as the SPL's brightest young manager while at St Johnstone, before going on to take charge of basket case Championship club Bristol City.
Former Dunfermline player Docherty, a former SFA Development Officer, is recognised as one of the best coaches in the game.
McInnes told RedWeb: "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.
"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."
Aberdeen fans group Dons Supporters Together said: "The new manager will have the full support of the DST board and we would urge all our members and supporters of Aberdeen to fully back our new manager in his efforts to take Aberdeen forward."
Aberdeen Mad wishes Derek and Tony the best of luck - and gees a cuppy mins!