The unanimous vote Tuesday came after city leaders said they favored the good of the Dallas suburb over protests from residents over parking lots being too close to their homes.
The decision affects several tracts along Central Expressway that Southern Methodist University has designated for the Bush library.
Mayor Blackie Holmes told homeowners that he sympathized with their concerns, but said the library will enhance the city.
Bush officials said steps have been taken to minimize the effect of parking lots, including putting them slightly below street level, using landscaping and routing traffic away from homes.
The library is expected to open in 2013.