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.
With the club suffering financial woes since their relegation to the second tier earlier in the same year, chairman Phil Gartside paid tribute to the work done by Freedman in challenging circumstances.
"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."
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