Biofunctionalized micro- and nanoparticles are important for a wide range of applications, but methodologies to measure, modulate, and model interactions between individual particles are scarce. Here, we describe a technique to measure the aggregation rate of two particles to a single dimer, by recording the trajectory that a particle follows on the surface of another particle as a function of time. The trajectory and the interparticle potential are controlled by a magnetic field. Particles were studied with and without conjugated antibodies in a wide range of pH conditions. The data shows that the aggregation process strongly depends on the particle surface charge density and hardly on the antibody surface coverage. Furthermore, microscopy videos of single particle dimers reveal the presence of reactive patches and thus heterogeneity in the particle surface reactivity. The aggregation rates measured with the single-dimer experiment are compared to data from an ensemble aggregation experiment. Quantitative agreement is obtained using a model that includes the influence of surface heterogeneity on particle aggregation. This single-dimer experiment clarifies how heterogeneities in particle reactivity play a role in colloidal stability.