Police fired tear gas to disperse the “yellow vests” who retreated to a bridge, throwing objects on the road, an AFP photographer at the scene said.
“The autoroute is now being cleaned to allow traffic to resume normally,” local authorities said.
France borders the Catalan region of Spain, and the French protesters were joined by dozens of Catalan pro-independence activists, also wearing yellow vests.
The separatists often block highways to protest against Madrid's rejection of Catalonia's independence referendum in October 2017.
Even though their goals are different, “this demonstration at the Boulou (toll booth) is symbolic, it shows the solidarity between the Spanish Catalans and the French,” said Marcel, a 49-year-old winegrower.
Roadblocks by protesters were also reported on autoroutes near the border with Italy and at a bridge in Strasbourg near the German border.
A driver died overnight when his car slammed into the back of a truck stopped at a roadblock set up by “yellow vest” protesters at an autoroute entrance in Perpignan on the Mediterranean coast, prosecutor Jean-Jacques Fagni told AFP.
There have now been 10 deaths related to the protests since they began on November 17.
In Paris, the scene of violent clashes during previous demonstrations, around 800 protesters joined rallies scattered around the city, police said at mid-day.
But the French capital's iconic Champs-Elysees avenue was calm, with most shops except for some luxury boutiques open for business in the busy weekend before Christmas.
David Delbruyere, 48, was one of about 20 protesters near the Arch of Triumph, the fifth time he has come to the French capital for a demonstration as he remains “disgusted” with conditions in France.
Paris police said 65 people had been arrested, including a “yellow vest” leader, Eric Drouet.
Authorities were also stationed at the Palace of Versailles outside Paris which has been closed to visitors over fears of unrest.
A Facebook event organised by Drouet had listed thousands of people “interested” in joining the Versailles demonstration but only around 60 have shown up.
Further demonstrations of several hundred “yellow vests” were reported in Lyon, Marseille, Rouen and Bordeaux.
And in Angouleme in southwest France, a puppet effigy of President Emmanuel Macron was decapitated Friday night during a “yellow vest” protest, regional authorities said Saturday.
Meanwhile, police stepped in with tear gas to disperse around 80 protesters who had gathered Saturday outside Macron's home in the Channel coast town of Touquet.
The number of protesters has however fallen significantly since last week, when Macron, a pro-business centrist, gave in to some of their demands.
Since the peak on November 17 with 282,000 demonstrators, the turnout has fallen to 166,000 on November 24, 136,000 on the first and eighth of December, 66,000 on December 15 and 23,800 Saturday.
The movement characterised by the high-visibility yellow vests worn by the protesters originally started as a protest about planned fuel tax hikes, but has morphed into a widespread demonstration against Macron's policies and top-down style of governing.
On Friday evening, the French Senate approved Macron's measures to help the working poor and pensioners — just hours after they were adopted by the lower house of parliament — which aim to quell “yellow vest” anger and should come into force early in 2019.