Assistant Tony Docherty has also moved on and Paul Sheerin will take charge of the team for the rest of the season, supported by Barry Robson and Neil Simpson.
The former St Johnstone boss took over from Craig Brown and ended the club's 19-year trophy drought when they beat Inverness CT in the 2013/14 League Cup final.
They were twice runners-up in that competition, were also Scottish Cup runners-up during McInnes' time in charge and consistently finished near the top of the table.
However, the Dons have scored just one goal in their last nine matches and are fourth in the Premiership, three points behind Hibernian and having played a game more.
Chairman Dave Cormack told the club website: "During his time in charge, Derek raised the bar and delivered a level of consistency not seen at the club for many years, qualifying for Europe each season, and delivering a memorable Scottish League Cup win at Celtic Park in season 2013/14 with 43,000 Dons fans in attendance.
“Clearly, results since the turn of the year have been disappointing and frustrating for everyone. Derek and I reviewed where we were and agreed this was the right time for him to step down. The club now has the opportunity to appoint a new manager ahead of the new season where, with a number of players out of contract, we have work to do to build a competitive squad.
“Derek and Tony leave with our thanks and gratitude for what they have achieved during their tenure. We wish them well for the future.”