The growth of mega-cities within the developing world has presented extreme challenges to ensuring the fundamental well-being of the general population and providing basic access to social services for all, especially adequate housing. Urban change in the mega-city has been particularly rapid and has involved a complex interaction between multiple actors at multiple levels. Tracing the patterns of urban development within this context is complex and involves incorporating the interactions between civil society, markets, and the state, operating at both micro and macro levels. Of key importance is the manner and degree to which the interaction or isolation between different agents shapes development patterns. This dissertation examines how residential segregation in Latin American cities in general, and Santiago, Chile in particular, is influenced by shifts in policy and planning and how advanced research methods can expose the linkages between social segregation, urban planning structures, and housing production. The primary goal of the research is to examine the nature of socio-spatial segregation in Metropolitan Santiago and the role that urban planning and formal housing provision plays in (re)producing or reducing the separation of different social groups. Santiago presents an ideal case for analyzing complex urban systems as it has developed under a strongly centralized state with formal housing provision processes and mature urban planning programs. While the physical patterns of socio-spatial segregation are broadly similar to many other Latin American cities, unique differences have emerged. Using a mixed-methods approach, the dissertation relates the policy and planning of housing programs, analytic evaluation of segregation patterns, and the simulation of segregation processes over time. The patterns and processes of socio-spatial segregation in Santiago are analyzed in detail via the macro- and micro-level structures of housing provision and urban planning. The central methodological contribution of the research is the employment of exploratory and simulation approaches, whereby formal methods that reinforce or reduce segregation are examined within a multi-level cellular automata model. The results of the dissertation suggest that patterns of segregation in Santiago are spatially and temporally heterogeneous, pointing to a complex relationship between the processes of urban governance, planning, and housing production.