A Cap Metro spokesperson says it happened on the driver's route near Riverside and Burton.
The driver was taken to the hospital with non life-threatening injuries and has since been released.
Two other passengers were on board at the time. Fortunately, they were not injured.
Cap Metro it does not believe its bus was the intended target, instead it appears this was a result of an altercation between two other vehicles.
Austin police are investigating.
"We are very fortunate and grateful that our operator is doing okay this morning after this terrifying ordeal. Our team has been in contact with him, and he’s now home resting," said Cap Metro. "We cannot stress enough, the important role our team has in our community, but our staff deserves to feel safe while at work."