Video taken by people inside the building showed huge flames.
Firefighters arrived on scene at Polytech where explosions heard earlier inside campus.
After daybreak rubber bullet casings and spent gas canisters lay on the road in front of the university entrance.
Goggles sitting in a pool of blood had been abandoned in a hurry.
Police had been seen dragging protesters away from the university after grabbing them near its entrance.
Many of the volunteer medics who would usually assist injured protesters had been arrested by police earlier as they tried to leave the campus.
The sound had been ferocious as special forces police had charged onto the road outside the main entrance firing rubber bullets and sponge rounds at protesters.
Protesters on balconies threw petrol bombs at police.
Throughout the night a pattern had emerged of the police water cannon firing at protesters but then retreating after being pelted with flaming projectiles. Protester Catapults on the corner of the campus had appeared to keep police back.
But when they finally charged the riot police came from a different direction and out of range of the catapult.
Later in the morning students tried to leave the university but many were arrested.
At least 40 were arrested near a hotel in the university precinct,which had been surrounded by a police cordon the evening before.
Journalists leaving the campus were lined against a wall by riot police as their bags were searched and details of their identity documents and passports recorded.
The fires and police action followed a tense night at the university,when police used a live Facebook broadcast to warn that officers would fire live ammunition if protesters did not stop targeting police,Radio Television Hong Kong reported.
A single live round was fired at 10.20pm near the People's Liberation Army barracks when a vehicle did not stop,police said.
The report of live fire came as police retook the roads on three sides of a heavily fortified Hong Kong university building as fears - later realised - rose inside the Polytechnic campus that riot police would charge it.
Chanting from the nearby Chinese barracks could be heard but the PLA stayed in its barracks.
Earlier in the evening,a police armoured vehicle tried to drive through barricades on the road to the university that overlooks a major cross harbour tunnel.
Protesters threw petrol bombs at the vehicle,setting it on fire,and forcing it to retreat.