The Dons boss was expected to seal a move to Ibrox after missing training for the last two days for reported talks with Pittodrie chairman Stewart Milne.
A former Rangers player, McInnes was interested in speaking to the Ibrox outfit and admitted that he "had a lot to consider" but has ultimately decided to stay put at Aberdeen.
In a statement, the Dons said: "Following weeks of speculation, Aberdeen Football Club can confirm that the management team of Derek McInnes and Tony Docherty will be remaining at Pittodrie."
McInnes added: "I've had a lot to consider over the last couple of days and I appreciate it's been a testing time for everyone, including my family, and I'm pleased to be now totally focusing on purely on-the-field matters."
McInnes and Docherty signed new contracts until 2020 in July after the former turned down the opportunity to take over at Sunderland.