A major bottleneck in search-based program synthesis is the exponentially growing search space which makes learning large programs intractable. Humans mitigate this problem by leveraging the compositional nature of the real world: In structured domains, a logical specification can often be decomposed into smaller, complementary solution programs. We show that compositional segmentation can be applied in the programming by examples setting to divide the search for large programs across multiple smaller program synthesis problems. For each example, we search for a decomposition into smaller units which maximizes the reconstruction accuracy in the output under a latent task program. A structural alignment of the constituent parts in the input and output leads to pairwise correspondences used to guide the program synthesis search. In order to align the input/output structures, we make use of the Structure-Mapping Theory (SMT), a formal model of human analogical reasoning which originated in the cognitive sciences. We show that decomposition-driven program synthesis with structural alignment outperforms Inductive Logic Programming (ILP) baselines on string transformation tasks even with minimal knowledge priors. Unlike existing methods, the predictive accuracy of our agent monotonically increases for additional examples and achieves an average time complexity of $\mathcal{O}(m)$ in the number $m$ of partial programs for highly structured domains such as strings. We extend this method to the complex setting of visual reasoning in the Abstraction and Reasoning Corpus (ARC) for which ILP methods were previously infeasible.