The Addicks won their opening game of the new League One season at home to Leyton Orient, but have since lost five matches in a row across all competitions.
Charlton were eliminated from the EFL Cup in the first round at the hands of Newport County earlier this month, and then went on to lose to Peterborough United, Bristol Rovers and Port Vale in League One, with the latter two of those matches coming at The Valley.
Holden's final match in charge proved to be Saturday's 2-1 defeat at Oxford United, when Charlton conceded an 85th-minute goal to lose against the league leaders.
That defeat left them 19th in League One, one point clear of the relegation zone after five games of the campaign.
Holden's assistant Danny Senda and goalkeeping coach Glyn Shimell have also been sacked by the club.
"I would like to thank Dean and his staff for their hard work and dedication and sincerely wish them all the best in their future careers," said Charlton chairman James Rodwell.
"Dean's work in steering the club clear of relegation last season should not be forgotten, nor his development of many younger players."
Jason Pearce, assisted by Anthony Hayes, will take the reins of the first team while the club search for a permanent successor.
Should a new boss not be appointed before then, their first match at the helm will come at home to Fleetwood Town next Saturday.
Holden spent eight months in charge at The Valley, winning 12, drawing five and losing 15 of his 32 matches as manager.