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Starting from the Color Glass Condensate (CGC) cross section for dijet production in proton-nucleus collisions we derive a transverse-momentum-dependent (TMD) factorization formula for small transverse-momentum imbalance of the jets and for finite number of colors. For the eight TMD distributions appearing in the cross section we determine their operator definitions at small-x as CGC correlators of Wilson lines and we study their JIMWLK evolution. We find that at large transverse momentum the universality of TMDs gets restored. We also discuss an extension of the approach to generalized TMDs (GTMDs) that can give an insight into the angular correlations between impact parameter and dipole size in the CGC framework.