Footage posted online, which has not yet been verified, shows a group jumping from the ledge at the top of a building onto a balcony beneath them in an attempt to flee.
Police can be seen moving along the street of the building while sirens and loud bangs can be heard in the background of the video.
An image, which has not yet been verified, also appeared to show students clinging onto the outside wall of the university building, on a narrow ledge several storeys up.
University staff were told to "stay put", barricade themselves in rooms and turn off the lights, news agency Reuters reported.
The suspected gunman, whose name has not been released, also died in the shooting.
His father has since been found dead.
Police believe the suspect killed his father in his home town of Hostoun, just west of Prague, earlier in the day, and that he had also been planning to kill himself.
The suspect suffered "devastating injuries" but it was not clear if he killed himself or was shot dead in an exchange of gunfire with officers, the police chief said, adding that there was "nothing to suggest that he had an accomplice".
Interior Minister Vit Rakusan said investigators do not suspect a link to any extremist ideology or groups. The Czech government declared December 23 a national day of mourning, Prime Minister Petr Fiala said on Thursday.