A government spokesman has denounced those participating in the rallies, calling them hard-liners who only want to bring down the government.
The incident at the ministry for relations with parliament on Rue de Grenelle in central Paris occurred on Saturday afternoon after violence flared in parts of Paris during the latest yellow vest protests.
That's a steep decline from the first demos, which saw tens of thousands of protesters throughout the country toward the end of previous year.
Further confrontations between police and protesters took place in other cities around France, with tear gas fired in Bordeaux and in Rouen, Normandy.
As darkness fell, officers dispersed scores of yellow vests gathered on Paris's Avenue des Champs-Elysees. "For her, it's about surviving", said one protester, 58-year-old Ghislaine.
Smoke and tear gas wafted above the Orsay Museum and the gold dome of the French Academy as riot police, almost invisible at the start of the demonstration, moved front and centre when protesters deviated from an officially approved path.
President Emmanuel Macron did not specifically refer to the incident, but tweeted his condemnation of the "extreme violence" against "the Republic, its guardians, its representatives and its symbols".
Police boats patrolled the river while beyond the Seine, motorcycles and a auto were set on fire on the Boulevard Saint Germain, a main Left Bank thoroughfare.
Five police were hurt and 11 people arrested, local authorities said, adding several cars were torched and shop windows broken.
Demonstrators wearing yellow vests hold banners next to burning barricades near the Champs-Elysees during a yellow vest protest in Paris, Jan. 5, 2019.
They have been concentrated on Saturdays, after first erupting on November 17 following a campaign spread on social media.
Faced with record low popularity ratings, Macron is expected soon to set out his plans for the coming months.
Protesters were looking to breathe new life into the yellow vest movement as numbers of participants has fallen since the first Saturday protest in mid-November. One known figure in the movement, Eric Drouet, was detained overnight this week for allegedly organizing an illegal demonstration.
He initially refused to make any concessions, but in mid-December, after weeks of violence, he scrapped the planned fuel tax hike and promised extra cash for minimum wage earners as well as tax cuts for pensioners.