Topological objects with skyrmionic textures in ferroelectrics, i.e., polar skyrmions, are promising technological paradigms in next-generation electronic devices. While breakthrough discoveries of stable polar skyrmions approximately ten nanometers in size have been very recently witnessed in complex systems, such a nontrivial topological order in ferroelectrics inevitably disappears below the ferroelectric critical size of several nanometers. Herein, we propose a strategy to overcome this limitation and achieve ultrasmall and isolated polar skyrmions by engineering excess-electron polarons in otherwise nonferroelectric SrTiO3 heterostructures. Our first-principle calculations demonstrate that a polaron localized at a SrTiO3 surface induces a Neel-type polar skyrmion as small as 1.8 nanometers attributed to the effect of atomic-scale surface roughness. Furthermore, we show that this polar topological structure is tunable by the choice of heterostructures and by the mechanical approach, which undergoes a phase transition to a meron state in the twisted boundary and to an antiskyrmion state in the surface with external shear strain, respectively. Such ultraminiaturization of skyrmions and their transitions unexpectedly unravels the formula of ultrasmall topological orders originating from the interplay between an electron polaron and structural symmetry breaking, which is completely different from the common mechanism of geometric confinement for larger-scale skyrmions. Our results not only provide a mechanism for the exploration of polar skyrmions and their rich topological transitions but also hold potential for ultrahigh-density memories.