Noun phrases and Relation phrases in open knowledge graphs are not canonicalized, leading to an explosion of redundant and ambiguous subject-relation-object triples. Existing approaches to solve this problem take a two-step approach. First, they generate embedding representations for both noun and relation phrases, then a clustering algorithm is used to group them using the embeddings as features. In this work, we propose Canonicalizing Using Variational AutoEncoders and Side Information (CUVA), a joint model to learn both embeddings and cluster assignments in an end-to-end approach, which leads to a better vector representation for the noun and relation phrases. Our evaluation over multiple benchmarks shows that CUVA outperforms the existing state-of-the-art approaches. Moreover, we introduce CanonicNell, a novel dataset to evaluate entity canonicalization systems.