The Cobra squad members, tasked with protecting an official, were attacked with sticks and flares by protesters, despite identifying themselves as official forces.
A soldier fired into the air to disperse the attackers, an action described as proportional by authorities.
Serbian President Aleksandar Vucic reported that more than 60 civilians and 16 police officers were also injured during the overnight riots in Novi Sad and Belgrade.
Protesters vandalized the headquarters of the ruling Serbian Progressive Party (SNS) with stones and incendiary devices.
Interior Minister Ivica Dacic warned that those responsible will be arrested within 48 hours.
Vucic downplayed the scope of the protests, which saw some 3,000 participants in Belgrade, while former Prime Minister Miloš Vučević promised to defend party headquarters.
Political tensions in Serbia are escalating following the recent elections, which were contested by the opposition.
The Balkan country is experiencing a climate of polarization that could intensify in the coming weeks.
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