Run them down with cavalry!
You can try tactics to get them to engage one (or more) non-cav (or even cav) units, then hit with cavalry from another direction.
However, often you can't avoid "the chase", which is a pain if you want to avoid nagging injuries & deaths of your own troops in the process. The best way to describe how I handle mobile skirms (incl. eastern, not just Numidia) is like a Texas cattle drive. I "herd" them with my Equites (or light cav, if using a non-Roman civ). I click on the far edge of the map, parrallel to the direction of flight, and do not try to engage units of similar speed, then I make "cuts" (quick change of direction, momentarily, toward the unit, even if I cannot get to grips) to 'steer' them to a map edge. Units, even infantry, can be used to converge to the expected point of battle from near or far, all you need to do is mentally compute the correct intercept vector, given the speed differential, to know where they will meet (I try to make that point on a map edge to avoid continued enemy flight). Once a unit (of mine) strongly engages the enemy being herded, they will be forced to stop flight, and fight. If it is an Equite unit that is engaging a more powerful (numeric or quality), like an eastern general (or FL), then you better have good timing with more units, esp. your slower General unit(s) or infantry, or else...
Naturally, it takes time and micromanagement to hunt down mobile skirmishing units, and since I personally rarely have battlefield numerical superority (except at the end of the battle), I have to prioritize when my cav units can be turned loose on 'the cattle drive.' Sometimes, they must fight at the main lines under fire in order to ensure the rout of enemy infantry, for instance.
The guiding method for making these decisions, for me, is experience (e.g., often a gut guess) of knowing whether I will take more overall casualties by routing the main enemy battle line whilst being pelted, then dealing with the skirms, or visa versa. It is also a consideration where on the battlefield the main line is, and likely direction of flight of routed enemy (can I hunt down some skirms, and still turn to hunt down the routed enemies before they can exit the battlefield?).
Literally, Good hunting...