The Government said it had rejected the proposal after a month-long public inquiry, which saw campaigners voice concerns about the impact the Battersea scheme would have on the neighbouring community.
Minerva’s application, which included two towers 32 and 42 storeys high, was refused because of the height of the tall buildings.
Salmaan Hasan, Minerva chief executive, said: “We are naturally disappointed by the Secretary of State’s decision and remain committed to our Ram Brewery and Buckhold Road sites which represent a rare opportunity to regenerate Wandsworth Town Centre.
“However, the Secretary of State has given a positive response to many aspects of the scheme and given guidance as to what is likely to be acceptable.
“We will now consider the information and guidance in the Secretary of State’s response and review our options as we look to move the scheme forward.”
The scheme comprises 1,036 apartments and 238,000 sq ft of retail, restaurant and other commercial accommodation.
Wandsworth Council granted planning consent at the end of 2008 but the scheme was called in by the previous government in February 2009.
The Health and Safety Executive (HSE) welcomed the decision after earlier advising Wandsworth to block the plan on the grounds it would harm public safety.
HSE’s Director of Hazardous Installations, Gordon MacDonald, said: “The proposed development site is very close to the Wandsworth Gasholder station.
“In the event of a major accident, it would have been difficult to evacuate people rapidly from the upper levels of the proposed very tall tower blocks.”