The former Manchester United captain wants to build the futuristic four-bedroom property on greenbelt moorland between Bolton and Bury.
The partially-underground house was labelled a “Teletubbies” home by teammates because of its petal-shaped design.
The planning committee approved the development by 12 votes to nine.
The application will now be referred to the Government Office for the North West for consideration.
The 36-year-old plans to have the kitchen in the flower’s stem, with its petals being bedrooms, bathrooms, a garage, a children’s play area and a swimming pool.
The planning application was turned down when it went before the planning committee last June.
Officers from Bolton Council recommended its approval because of “its exceptionally high quality of design” and “sensitive relationship with the surrounding landscape”.
But committee members ignored the report’s advice and voted 14-6 to refuse the application.
The application was re-submitted with the height of a wind turbine lowered.
A council spokeswoman said: “The committee has approved the plans and the application will now be referred to the Government Office for the North West (GONW) for consideration.
“Should GONW consider it justified the Secretary of State for Communities and Local Government has the power to intervene, and call in the application for him to consider.
“However, if the scheme is approved by GONW and the scheme is not called in for review, then the application will be referred back to the council. The Director of Development and Regeneration will then ratify the decision, under delegated powers.”