You can pay missed tolls online without a violation fee. You must make payment within the grace period of time allowed by the state where the missed toll occurred.
Details on the documentation required when you submit an online payment vary from state to state. Some states, such as Florida, may require you to set up a prepaid account in order to pay online. Other states, such as Illinois and New York have no such requirement. New York issues an unpaid toll slip with a transaction number which must be noted with your payment while Illinois requires that you note the location of the toll booth where the toll was missed.