The university decided to end the ceremony immediately after degrees had been conferred by Vice Chancellor Rocky Tuan because of "special circumstances", the South China Morning Post quoted a CUHK spokeswoman as saying.
"Verbal disputes broke out between those with different opinions, graffiti was sprayed on the campus and there were disruptions while the ceremony was taking place.
"Therefore, after awarding all the degrees, the university decided to suspend the ceremony immediately."
When the national anthem was played at the beginning of the ceremony, many students turned their backs on the stage, and some could be heard chanting slogans such as "liberate Hong Kong, revolution of our times".
Many students also wore masks and held up banners.
Thursday's development comes a day after chaos erupted on Wednesday evening at a dialogue forum hosted by the president of Hong Kong University of Science and Technology Wei Shyy, when a student believed to be from the Chinese mainland pushed a Hong Kong student to the ground.
The trigger for the clash was unclear but the incident left at least four students injured.
The Hong Kong protests, which have been drawing massive crowds since June following a contentious proposed extradition law, have mutated into a movement that seeks to improve the democratic mechanisms that govern the city and safeguard the region's partial autonomy from Beijing.
However, some demonstrators have opted for more radical tactics than peaceful civil disobedience and violent clashes with the police have been frequent.
( With inputs from IANS )