The new deal come just over a month after the 46-year-old rejected an offer to become new Sunderland manager.
McInnes told the club’s official website: “We’re delighted to extend our contracts and both Tony and I are looking forward to the season ahead.
“We’ve still a lot to do both on and off the pitch and as I’ve mentioned on several occasions I want our tenure here with Aberdeen to be remembered fondly as a successful period and one where we were winning trophies.
“I am committed to trying to bring more success to the club and with the excellent squad of players we have and the backing of our brilliant supporters, it is important we keep driving forward both on and off the pitch and maximise our full potential as a club.”
