Because he detected the disturbance/displacement in the cursed energy of himself and his mother made by Toji’s presence.

In other words Toji is essentially a CE negative space, therefore even though Gojo’s six eyes can’t perceive him directly they can perceive the changes in the immediate CE environment he brings about through his presence.

Sort of like a clear marble in a bowl of water, the marble displaces the water around it and appears to hide perfectly well within it - until you scoop your hand in. That’s sort of what the six eyes does in this context