A critical first even in mammalian development is construction of the inner cell mass and trophoectoderm surrounding it. Using imaging and computational modeling, we show that by controlling the pace of cell fate specification, the embryo creates a crucial window of time where regulatory noise promotes accurate organization of these structures. Imaging results further indicate different gene products (Oct4 and Cdx2) exhibit significantly different levels of noise variation. Surprisingly, this asymmetry provides a novel means to balance the positive and negative influence of stochasticity. More generally, these results indicate noise has a positive role in spatially organizing the embryo.