Al Jazeera's Mariana Sanchez said the situation at the country's biggest university turned chaotic as people tried to locate the shooters whom witnesses said wore ski masks or T-shirts over their heads.
She said some of the students were seen barricading the entrance to a building to protect themselves.
A video aired by Globovision later showed armed men, some riding motorcycles, entering the same building with one of them firing a handgun in the air.
The students had earlier joined about 80,000 people to protest against an upcoming referendum over radical constitutional reforms.
The changes, if approved in the referendum on December 2, will allow Hugo Chavez, the president, to remain in power indefinitely.
|Protesters demanded the constitutional|
changes be suspended [Reuters]
Pedro Carreno, the justice minister, blamed students, university authorities, opposition parties and the media for the violence.
"We want to urge the media to reflect, to stop broadcasting biased news through media manipulation, filling a part of the population with hate," he said on national television.
He said angry students surrounding the building wanted to lynch those inside, but no details were provided.
Protesters are demanding the referendum be suspended, saying the amendments will erode civil liberties in one of South America's oldest democracies and give Chavez unprecedented power to declare emergencies.