UV light damages DNA by inducing cyclobutane pyrimidine dimers (CPDs) and other lesions that must be efficiently repaired to avoid cell death or mutagenesis. While essentially all species can repair CPDs via nucleotide excision repair (NER), many species, including bacteria, yeast, and other eukaryotes, also utilize photolyase enzymes to repair UV damage. How these disparate repair pathways function in concert to repair UV damage across a eukaryotic genome packaged in chromatin remains unclear. Here, we use our CPD-seq method to map repair of CPD lesions by NER and photolyase across the yeast genome. Our data indicate that NER repairs damage throughout the genome, and that this repair is modulated by chromatin and histone acetylation. CPD lesions are more rapidly repaired by yeast photolyase, but this repair is significantly inhibited when damage is located in certain classes of transcription factor binding sites or in nucleosomes. Repair of damage in nucleosomes is particularly inhibited when CPDs are located at the 3’ side of the nucleosomal DNA or at minor-in rotational settings. While photolyase efficiently repairs the non-transcribed strand (NTS) of yeast genes, repair of the transcribed strand (TS) is inhibited. Genome-wide analysis of UV-induced mutations in NER-deficient, photoreactivated yeast revealed a striking enrichment of mutations along the TS of yeast genes. Taken together, these data indicate that inhibition of photolyase repair along the TS, likely due to occlusion of CPDs by RNA polymerase II stalling, promotes UV mutagenesis.