Brittany Higgins' case sparked a sweeping review that identified a "boys club" culture in parliament in which sexual harassment is rife.
The apology in parliament on Tuesday was also for others who have suffered sexual misconduct or bullying there.
Mr Morrison has previously faced criticism over his responses.
Ms Higgins, a former staffer for two ministers, was seated in the House of Representatives public gallery to watch the apologies by the prime minister, the opposition leader and others.
"I am sorry, we are sorry. I am sorry to Ms Higgins for the terrible things that took place here. The place that should have been a place for safety, that turned out to be a nightmare," Mr Morrison said.
"I am sorry for far more than that. All those that came before Ms Higgins … but she had the courage to speak, and so here we are."
Ms Higgins helped inspire tens of thousands of people to join protests last year after coming forward with her allegation.