Several hundred protesters pelted police with stones and destroyed toll booths before setting them alight during the demonstration near the Morina border crossing on Saturday. Police said 14 officers were injured.
Twenty-three protesters were arrested, 11 of whom were given prison terms whose length would be determined later.
They appeared before the court in the capital Tirana under tight security in place to prevent more violence.
Following the ruling, the rightwing opposition Democratic Party urged Albanians to begin "civil disobedience" and to "rise up" against the government led by socialist Prime Minister Edi Rama.
The highway, an important route for trucks trading with neighbouring Kosovo, was built in 2009 and was free until the weekend.
New tolls of between 2.5 to 22.5 euros ($3 to $28), to fund road maintenance, came into force on Sunday along the 100-kilometre (60-mile) long highway.
The cost is significant in a country with an average monthly salary of around 350 euros.
It is seen as a particular burden in Kukes, where the toll barrier is located, which is one of the poorest regions in Albania.
"I urge the citizens to rise up against the regime of Prime Minister Edi Rama and to resist until his departure, in all possible ways and by all democratic means," Democratic Party leader Lulzim Basha said after the ruling.
He also encouraged his compatriots to start "civil disobedience, by refusing to pay taxes" and offered his support to a planned blockade of the country's roads on Thursday.
Rama accused the opposition of wanting to "use Kukes as a Molotov cocktail".
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