Encapsulated rejuvenators embedded in asphalt mixtures are a promising technology to extend the service life of asphalt pavements. However, their effects on the asphalt mixture’s performance still need to be properly understood. A recently developed three-dimensional discrete element method framework enables the evaluation of non-homogeneous distributions of the rejuvenator, closely resembling real conditions. This includes different scenarios involving capsule content and release efficiency. The presented numerical results show that the rejuvenator-to-mastic ratio and the number of rejuvenator-modified contacts influence the stiffness properties of asphalt mixtures. In cases where a homogeneous rejuvenator distribution is assumed, the three-dimensional DEM model predicts a significant reduction in the asphalt mixture’s stiffness that compromises the pavement’s performance. Simulations show that the diffusion effect needs to be considered for predicting the post-healed behavior of asphalt mixtures. For cases considering more suitable modified mastic amounts (less than 1.20 wt%), the effect on the asphalt mixture’s stiffness modulus is less pronounced, and the phase angle is not significantly affected. Additionally, the presented simulations suggest that the capsule content can be increased up to 0.75 wt%, and capsules with a release rate higher than 48% can be used without compromising the rheological performance of asphalt mixtures, possibly improving their self-healing properties. These numerical insights should be considered in future designs to achieve optimal post-healed behavior.