Topological phase in magnetic materials yields a quantized contribution to the Hall effect known as the topological Hall effect (THE), which is often caused by skyrmions, with each skyrmion creating a magnetic flux quantum ±h/e. The control and understanding of topological properties in nanostructured materials is the subject of immense interest for both fundamental science and technological applications, especially in spintronics. In this article, the electrontransport properties and spin structure of exchange-coupled Co nanoparticles with an average particle size of 13.7 nm are studied experimentally and theoretically. Magnetic and Hall effect measurements identify topological phase transitions in the exchange-coupled Co nanoparticles and discover a qualitatively new type of hysteresis in the topological Hall effect, namely Berry-phase hysteresis. Micromagnetic simulations reveal the origin of the topological Hall effect, namely the chiral domains with domain-wall chirality quantified by an integer skyrmion number. These spin structures are different from the skyrmions formed due to Dzyaloshinskii-Moriya interactions in B20 crystals and multilayered thin films and caused by cooperative magnetization reversal in the exchange-coupled Co nanoparticles. An analytical model is developed to explain the underlying physics of the Berry-phase hysteresis, which is strikingly different from the iconic magnetic hysteresis and constitutes one aspect of 21 st century reshaping of our view on nature at the borderline of physics, chemistry, mathematics, and materials science.