Many bacterial species have a nonhomologous end joining (NHEJ) system of DNA repair driven by dedicated DNA ligases (LigD and LigC). LigD is a multifunctional enzyme composed of a ligase domain fused to two other catalytic modules: a polymerase that preferentially adds ribonucleotides to DSB ends and a phosphoesterase that trims 3’ oligoribonucleotide tracts until only a single 3’ ribonucleotide remains. LigD and LigC have a feeble capacity to seal 3’-OH/5’-PO4 DNA nicks. Here we report that nick sealing by LigD and LigC enzymes is stimulated by the presence of a single ribonucleotide at the broken 3’-OH end. The ribo effect on LigD and LigC is specific for the 3’ terminal nucleotide and is either diminished or abolished when additional vicinal ribonucleotides are present. No such 3’ ribo effect is observed for bacterial LigA or Chlorella virus ligase. We find that in vitro repair of a double-strand break by Pseudomonas LigD requires the polymerase module and results in incorporation of an alkali-labile ribonucleotide at the repair junction. These results illuminate an underlying logic for the domain organization of LigD, whereby the polymerase and phosphoesterase domains can heal the broken 3’ end to generate the monoribonucleotide terminus favored by the NHEJ ligases.