What you need is called a net tie. Make a new component with a via-sized footprint and connect both nets to it on your schematic.
Net ties are useful when you need to keep connections between two nets limited to one point, like controlling digital and analog ground on mixed-signal designs.
Unfortunately I can't give specific instructions for KiCad as I am not familiar with their interface, but do some reading on net ties and you should be able to find what you need.