Miksic is now demanding a new vote count.
Sunday's vote was a "fraud and a slap in Croatian people's face", Miksic told the crowd that gathered briefly at the main Ban Josip Jelacic square.
A wealthy US-Croatian businessman, Miksic says he should have finished second in the election and be the one to face incumbent President Stipe Mesic in the run-off on 16 January.
A Euro-sceptic outsider on Croatia's political scene, he was the biggest surprise of the elections, placing third with 17.8% of the vote.
Centrist Mesic won 48.9% of the votes, and is to face Deputy Prime Minister Jadranka Kosor of the ruling conservative Croatian Democratic Union (HDZ) in the run-off.
Kosor garnered 20.3% of the votes, according to results from nearly all polling stations on Monday.
Stipe Mesic (L) and Jadranka
Kosor will face off for president
But Miksic complained he was not allowed to have his own observers within the electoral commission counting the votes.
He stressed exit polls had put him ahead of Kosor. But the electoral commission threw out his complaint.
In several other Croatian towns, Miksic's supporters gathered peacefully to protest against the election results, national radio reported.
Some thirty gathered in the Adriatic towns of Split and Zadar respectively, and several dozens in the northern town of Cakovec as well as in the eastern town of Slavonski Brod.
There were no incidents reported during the protests.
Miksic said he would file a complaint with the constitutional court.