"Vucic thief, you stole the elections!" a crowd of several thousand in Belgrade chanted, marching through the centre of the capital, AFP correspondents at the scene reported.
Led by several drummers, protesters blew whistles and carried placards saying "You are gone" and "You are not my president." One young man waived a big red flag with Che Guevara’s portrait.
Similar demonstrations were held in Novi Sad in the north and Nis in the south, Serbia's second and third largest cities, respectively, local media reported.
Vucic on Sunday won the presidential election in the first round with a clear majority, garnering 55 percent of votes, and will take office as president in late May.
It was not clear if any group was behind the protests as participants said they had no leader and were organised through the Facebook social network.
But their complaints echoed those of Serbia's opposition which had cried foul over an "unfair" election campaign that was marked by Vucic's omnipresence in the media. It also claimed that voters had been intimidated and threatened.
On Monday Vucic said that "everyone has a right to be unhappy with the election results."
"It is fine as long as it is peaceful," Vucic said.
His main rival, ex-ombudsman Sasa Jankovic who came second in the vote with 16 percent, supported the protest but urged participants to keep it non-violent.
"Dear young people on Belgrade streets, express freely your protest over unfair elections. Just (do it) non-violently and do not allow provocations. That is your right!", Jankovic wrote on his Twitter account.
And Luka Maksimovic, a 25-year-old satirist who ran as the fictional Ljubisa Preletacevic -- nicknamed "Beli" (White) -- and came third with 9.3 percent of the vote, called for protesters to remain calm and avoid "being used by (someone's) personal and party interests".
"So please take it easy and be smart," Maksimovic wrote on his Facebook page, while denying any involvement in the protests or calls to join them.
"Do not force me to stand in front of these youngsters. I have finished my mission, showed that it is possible (to win votes without a political party) so now make local movements and change things from the root, not from the top," he wrote.
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