The girls, both 14, said the driver called them "sickos" after a female passenger complained about their kiss. The driver then stopped the bus along the street and forced them off.
"Removing the girls from the bus was not consistent with our policy," TriMet General Manager Fred Hansen said Wednesday. "I want to reiterate that we welcome all riders on our system."
The 64-year-old driver also violated company policy that requires operators to call for assistance before removing any minors, TriMet said in a statement.
The driver, an 11-veteran who was not identified, will be disciplined, TriMet officials said, though no details were released.
"TriMet sincerely apologizes to the girls and their families for this incident," Hansen said in the statement.
The mother of one of the girls, Ronnda Zezula, welcomed the apology.
"The only thing I had a problem with is they didn't really address why the driver broke those policies," Zezula said. "He knew it was wrong. He's been a driver for 11 years."
She also said she wished the agency had made the extent of the disciplinary action public to show it will not "be just a slap on the wrist."
Zezula said the family has been encouraged to consider a lawsuit, but they will "have to mull it over."