The energy is coming from the electromagnetic field.
Electromagnetic fields carry an energy. The energy per unit volume is
$$
u = \frac{1}{2} \epsilon_0 E^2 + \frac{1}{2 \mu_0} B^2
$$
where $E$ is the electric field and $B$ is the magnetic field. For two charges at rest $B=0$ but $E \ne 0$.
To get the total energy in the field you have to integrate this $u$ over all space. This cannot be done if you think of the charges as point-like (because the answer comes out as infinity), but for the purpose of doing this calculation you can just model the charges as if they were each a very tiny ball, and then you get sensible results. When the charges move apart the field very near each charge does not change much, but the field everywhere else does. One finds that, overall in the case you asked about, the final field energy is smaller than the initial energy, and this is where the energy given to the kinetic energy of the charges came from.
When we teach this at high-school level, we don't normally talk about field energy, but instead we talk about 'potential energy' of the charges. This is two ways of talking about the same thing.