To do this, create a new invoice that will essentially tax the customer for nothing (accounting-wise).

1. Create an item to use for this purpose as a sort of wash item. Probably an other charge item. Use either a sales account or misc account. (The net impact to the account will be 0.00.)

2. Use the item on a new invoice. Enter it twice, once as a positive, and once as a negative, where only the positive instance is taxable.

When complete, it should look like this: