We numerically simulate the creation process of two-dimensional skyrmionic excitations in antiferromagnetic spin-1 Bose-Einstein condensates by solving the full three-dimensional dynamics of the system from the Gross-Pitaevskii equation. Our simulations reproduce quantitatively the experimental results of Choi et al. [Phys. Rev. Lett. 108, 035301 (2012)] without any fitting parameters. Furthermore, we examine the stability of the skyrmion by computing the temporal evolution of the condensate in a harmonic potential. The presence of both the quadratic Zeeman effect and dissipation in the simulations is vital for reproducing the experimentally observed decay time.