Bolton have won just once in the league this term and sit second bottom in the table following Wednesday's 4-0 defeat to fellow strugglers Fulham.
The loss at Craven Cottage proved to be the Scot's last game in charge, having been appointed in 2012 after a strong spell at Crystal Palace.
"Dougie has worked tirelessly off the field to improve the infrastructure of the football club," he said in a statement on the club's official website.
"Unfortunately, recent results on the pitch have not reflected all his work off it.
"The club has faced a difficult time following our relegation from the Premier League and Dougie has helped to restructure the club in order for it to become successful again under ever-tightening constraints.
"I would like to thank Dougie personally for all his commitment and efforts for Bolton Wanderers."
