The university considered revoking the 2004 award following a request from a member of staff.
Cardinal O'Brien resigned from the Archdiocese of St Andrews and Edinburgh in 2013 after several priests accused him of inappropriate behaviour.
He admitted his sexual conduct had at times "fallen below the standards expected of me'', and he no longer plays a public role in the Catholic Church in Scotland.
A St Andrews committee ruled that revoking the award would not change wrongdoings of the past and would be "no more than an empty gesture".
A statement said: "The Senate Business Committee recognises that universities award honorary degrees in good faith on the basis of evidence available to them at a point in time, that revocation cannot change or ameliorate the wrongs of the past and that, notwithstanding the very real hurt and loss caused by the actions of the honorand, it would be no more than an empty gesture.
"The committee also formally recorded its disapproval of the inappropriate manner in which the request had been brought into the public domain before any decision had been reached by SBC in what could be interpreted as an attempt to prejudice the decision-making processes of the committee."