Several of the protesters who had gathered near Sanaa University were wounded while others were arrested by the militiamen, the witnesses said.
The militiamen also attacked journalists and smashed their cameras.
They deployed heavily around the university to prevent any new protests.
The Houthi militia, who have controlled most of the capital since last September, overran the presidential palace last week prompting President Abdrabuh Mansur Hadi to tender his resignation on Thursday, shortly after Prime Minister Khalid Bahah quit.
Thousands of Yemenis took to the streets of Sanaa on Saturday in the biggest protest yet against the Houthis.
The Huthis still hold Mubarak and maintain a tight grip on the capital despite a deal struck late on Wednesday to end what authorities called a coup attempt.
The fall of Hadi's Western-backed government would raise fears of complete chaos engulfing Yemen, strategically located next to oil-rich Saudi Arabia and on the key shipping route from the Suez Canal to the Gulf.
Oxfam warned on Friday that 16 million people - more than half the population - were in need of aid in Yemen.
"A humanitarian crisis of extreme proportions is at risk of unfolding in the country if instability continues," the aid group said.
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