The Pestle can be equipped onto the Mortar by simply right-clicking it with the Pestle in your hand. This will then allow the Mortar to be able to grind items. However, it consumes one use per grind, so it must be replaced after some time.
Like most other equipment with durability, a damaged Pestle can be repaired to full durability through an Animator. The more that needs to be repaired, the greater the cost of fuel and crystal charge is in the animation process.