The Dutchman's departure comes after the team asked staff and riders to confirm whether they had any links to doping in the wake of the Lance Armstrong scandal.
Team Sky says De Jongh "disclosed that he had taken a banned substance earlier in his career as a professional rider."
Team principal Dave Brailsford says "he's been a highly-valued sports director and colleague over three seasons."
De Jongh's exit comes less than a week after American coach Bobby Julich left Team Sky after revealing he took EPO in his racing career.
Team Sky rider Bradley Wiggins won the Tour de France in July.