"Juan Orlando, dictator!" and "Get out of Honduras!" an estimated 500 marchers chanted, referring to conservative Juan Orlando Hernandez.
The Supreme Electoral Tribunal says Hernandez won the vote with an unbeatable 36.35 per cent lead after Sunday's presidential election, against 28.91 per cent for leftist Xiomara Castro, wife of ousted ex-president Manuel Zelaya.
It was the third day running that hundreds of students rallied to support Castro, who would be impoverished Honduras's first woman president if elected.
"If the votes say Xiomara won the election and her win is not acknowledged, then what you will have here is a major crisis," her running mate Juan Barahona told AFP.
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Zelaya said Wednesday that his wife and her Libre Party "have been robbed of their victory, and we are going to show it."
European Union and Organisation of American States observers called the voting process transparent and non-problematic.
Castro, who proposes "Honduran-style democratic socialism," wants to rewrite the constitution and "re-found" the country -- a move similar to the one that led to the coup that ousted her husband in 2009.
The clash between Hernandez and Castro brought new uncertainty to a deeply troubled country, also reeling from the wounds of the coup against Zelaya just four years ago.
Hernandez, who is also speaker of the legislature, said the people have spoken at the ballot box.
The governments of Colombia, Guatemala, Panama and Costa Rica congratulated Hernandez.
Nicaragua's leftist President Daniel Ortega also recognised Hernandez as the winner, while the United States recognised Hernandez's "irreversible" lead.