In response to the report, Dr Ian Mair, deputy chair of the university court, said: "It is evident from the report that there have been clear failings in financial monitoring, management and governance.
"While there were significant external factors, which have affected the higher education sector across the UK to varying degrees, the university's response to these, and responsible management of our finances, has fallen well short of the standards that everyone should have expected."
Dr Mair added: "I understand that this has been an extremely stressful time for staff and students and I offer my sincere apologies for all of the anxiety and uncertainty this situation has caused.
"You have all deserved better, and we can only work to make that the case from here on."
He said the court hoped to make an interim appointment of a new principal to replace Prof O'Neill in the next few days.
Prof O'Neill said it was with a "very heavy heart" that he had decided to step aside.
He said: "I have done all I can to set the university on a path to recovery, engaging with internal and external stakeholders to find the best way forward.
"I had hoped that we would be further along that path by now, and it will now be for others to steer that course into the future.
"I am truly sorry for the impact this financial crisis has had on many people, particularly our staff and students."