We report the measurement of near threshold neutral pion electroproduction cross sections and the extraction of the associated structure functions on the proton in the kinematic range $Q^2$ from 2 to 4.5 GeV$^2$ and $W$ from 1.08 to 1.16 GeV. These measurements allow us to access the dominant pion-nucleon s-wave multipoles $E_{0+}$ and $S_{0+}$ in the near-threshold region. In the light-cone sum-rule framework (LCSR), these multipoles are related to the generalized form factors $G_1^{pi^0 p}(Q^2)$ and $G_2^{pi^0 p}(Q^2)$. The data are compared to these generalized form factors and the results for $G_1^{pi^0 p}(Q^2)$ are found to be in good agreement with the LCSR predictions, but the level of agreement with $G_2^{pi^0 p}(Q^2)$ is poor.