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The fallout results from the news in January the company had overstated its oil reserves, causing a global backlash from investor groups which called for Watts' sacking. As recently as February 5, when he revealed Shell's annual financial results, Watts insisted he would not be resigning.
Comments from Shell indicated Watts held out until the last, with the board insisting he step aside.
"The resignations were tendered by the executive directors promptly on receipt of the indication of the board's wishes," a company spokeswoman was reported as saying.
Watts will be replaced by Jeroen van der Veer, the head of the company's chemicals unit.
Shares of Shell Transport & Trading Co. rose nearly 2 percent to 383.25 pence on the London Stock Exchange.
