The masterplan, drawn up by Arup Associates and Fletcher Priest, forms a key part of the development of the area, in time for the 2012 Olympics.
It borders the Olympic Park and the many of the new homes will form the Olympic Village.
The submission represents the culmination of years of designing and planning, which was both helped and hindered by the decision to award the 2012 games to London last year.
Stratford City is one of the biggest one-off developments in the capital's history. When completed, it will consist of 1.25 million m2 of retail, leisure and entertainment facilities, offices and hotels, plus 5,312 new homes - of which 3,000 will be used initially for the Olympic Village.
John Burton, Westfield's development director, said: 'The plans we have submitted bring forward creative, innovative and cost effective solutions for the design, construction and operational stages of Stratford City's development.
'We are conscious that these strategies and their implementation will create a new standard for major development projects.
'Work is already underway,' he added. 'We are on site doing preparation work and infrastructure design is well-advanced.'