Is my violation of university instructions and being late for lectures, despite the professor allowing me to do so and my passing the course, considered halal or بناء على باطل (built upon falsehood)?

If the doctor is not authorized to grant you an absence, then it is not permissible for him to cover up your violation of the conditions, because that is a betrayal of trust. However, if he is authorized to do so, then there is no blame upon either of you. And since you were not expelled and succeeded in the course, there is no blame upon you for continuing your studies at the university, and do not repeat such an act if it is prohibited.