The shooting was reported at 2:16 p.m., police said.
AC Transit spokesman Clarence Johnson said someone fired a gun at a Line 1R bus as it traveled east on International Boulevard between Ninth and 10th avenues.
The bus operator kept driving "to get out of harm's way," proceeding to 15th Avenue, Johnson said.
He said at least one passenger on the bus was hit by the gunfire.
"That person appeared to have been wounded in the shoulder," Johnson said.
Police spokeswoman Sgt. Holly Joshi said that when officers responded they also located a second victim.
The two victims, who are both men, were taken to a hospital with injuries that are not life-threatening, she said.
Johnson said that once the bus stopped, all of the passengers exited. The male driver was not hurt but was "very shaken," Johnson said.
Neither police nor Johnson had a description of the shooter or any details about what prompted the shooting.
The incident left bullet holes in two windows on opposite sides of the bus, but no bullets appeared to have hit the body of the vehicle, Johnson said.