The result, coupled with Barnsley's 2-0 win over Leeds, sent City rock-bottom of the Championship - and McInnes has paid the price after a run of three consecutive defeats.
Robins managing director Jon Lansdown told the club's official website: "This is a decision we felt we had to make for the good of the football club.
"Derek has been a pleasure to work with; he's disappointed but he understands the decision.
"We want to give ourselves the best possible chance of getting out of the situation we are currently in and we've got 20 games to do that."
McInnes took control at Ashton Gate in October 2011 having left St Johnstone to chance his arm in English football, and saved the club from relegation in his first season at the helm.
Assistant manager Tony Docherty has been asked to take first-team training on Monday.
Coventry City boss Mark Robins has been installed as the early favourite to succeed McInnes as Bristol City manager.