It happened around 4:30 p.m. Tuesday at 57th Street and Larchwood Avenue in the city's Cobbs Creek section.
Police say a 29-year-old was shot in the buttocks, a 56-year-old was shot in the back, and a 60-year-old suffered a graze wound to the side of her head. All three are listed as stable at an area hospital.
According to Philadelphia Police Chief Inspector Scott Small, this all started when three young males boarded the bus without paying at 19th Street and Oregon Avenue in South Philadelphia.
"They had some words with the driver. However, the driver pretty much shrugged it off," Small said of the confrontation.
At 57th and Catherine streets, the suspects got off, and that's when police say one of them fired four shots into the passenger's side of the bus.
"Everybody just started screaming, 'Stop the bus, stop the bus!' And obviously, he didn't stop the bus because the shooters were right there," recalled a passenger who identified herself as Tori.
"I thought I was going to die for a second, so it's just weird," she added.
There were more than 50 people on the bus when the shots rang out, including a shooting victim's child, Small said.
No other injuries were reported, and police say the passengers were able to flee to safety after the shooting.
The suspects were captured on the surveillance video but no images were publicly released Tuesday.
Officers are still trying to establish a motive. It's unclear if that earlier altercation with the bus driver played a role.
Anyone with information is asked to call police at 215-686-TIPS.