The role of dynamical pairing in induced fission dynamics is investigated using the time-dependent generator coordinate method in the Gaussian overlap approximation, based on the microscopic framework of nuclear energy density functionals. A calculation of fragment charge yields for induced fission of $^{228}$Th is performed in a three-dimensional space of collective coordinates that, in addition to the axial quadrupole and octupole intrinsic deformations of the nuclear density, also includes an isoscalar pairing degree of freedom. It is shown that the inclusion of dynamical pairing has a pronounced effect on the collective inertia, the collective flux through the scission hyper-surface, and the resulting fission yields, reducing the asymmetric peaks and enhancing the contribution of symmetric fission, in better agreement with the empirical trend.