Denham turned down P&O's £1 billion plans for three towers reaching up to 33 storeys in Waterloo last week. The Three Sisters development was backed by the London Borough of Lambeth but then called in by the government.
Denham agreed with the inquiry inspector that the buildings would have a negative impact on the historic skyline of the area. None "possess the balanced, sculptural or elegant qualities that are crucial to the success of tall buildings", his decision letter concludes.
However, Savills head of planning and regeneration Roger Hepher said: "This decision will cause confusion. Recent approvals of tall buildings at Doon Street and Blackfriars, together with the mayor's more conciliatory stance, have reassured property developers."
He continued: "The Three Sisters refusal is a salutary reminder that the right site and the correct design are fundamentally important."
Westminster City Council welcomed the rejection of the scheme. Deputy leader Robert Davis said the towers would have been a blot on the landscape for generations to come. "We are not against the principle of tall buildings, providing they are in the right place and do not damage important views, " he added.
Last week, Westminster and English Heritage gave up their fight against the 43-storey Doon Street scheme.
A P&O spokesman told Planning that the company is considering whether to appeal the decision.