California Highway Patrol officers put down road spikes to flatten the tires and get the bus to stop on Friday.
The driver faces charges including reckless driving, failure to yield, and grand theft.
Alameda County Transit spokesman Clarence Johnson tells a local television station that the bus was outfitted with a GPS system which allowed authorities to track it.
No one was on the bus or was injured. Johnson says the bus was parked, closed and locked at the terminal when it was stolen.