The complete structure revision of the RE2PdGe3 (RE = rare-earth metal) series revealed that Yb2PdGe3 is the only AlB2 ordered superstructure. Good-quality single crystals of this compound were successfully grown from molten indium flux, enabling accurate single-crystal investigations. Yb2PdGe3 crystallizes with the Ce2CoSi3-type structure in the hexagonal space group P6/mmm (no. 191) with lattice parameters a = 8.468(1) Å and c = 4.0747(7) Å. This structure is a four-order derivative of AlB2, composed of planar ∞2[PdGe3] honeycomb layers spaced by Yb species, located at the center of Ge6 and Ge4Pd2 hexagons. A superconducting transition is observed below the critical temperature of 4 K. A divalent state of Yb is deduced from magnetic susceptibility measurements below room temperature, which indicate an almost nonmagnetic behavior. A charge transfer from Yb to Pd and Ge was evidenced by the Quantum Theory of Atoms in Molecules (QTAIM) effective charges; polar four-atomic Ge-Pd/Yb and two-atomic Pd-Yb bonds were observed from the ELI-D (electron localizability indicator), partial ELI-D, and ELI-D/QTAIM intersections. The bonding interactions between Ge atoms within regular Ge6 hexagons are found to be intermediate between single bonds, as in elemental Ge, and higher-order bonds in the hypothetic Ge6H6 and Ge66- aromatic molecules.