Electoral court president David Matamoros made the announcement this evening, saying, "We have fulfilled our obligation (and) we wish for there to be peace in our country."
According to the court's official count, Hernandez won with 42.95 per cent to 41.42 for Nasralla, who well before the announcement had challenged the result and said he would not recognize it.
There was no immediate public comment by Hernandez, whose sister Hilda Hernandez, a Cabinet minister, died Saturday in a helicopter crash.
Earlier in the day Nasralla traveled to Washington to present what he called "numerous" examples of evidence of alleged fraud. He said he planned to meet with officials from the OAS, the US State Department and human rights groups.
Interviewed by UneTV during a layover at the Miami airport, Nasralla called Hernandez's re-election illegitimate and said he would ask the OAS to invoke its democratic charter against Honduras.
Former President Manuel Zelaya, a Nasralla ally, called for civil disobedience.
"May God take us having made our confessions because today the people will defend in the streets the victory that it obtained at the ballot box," Zelaya said.
In a statement, he urged police and the armed forces to "place themselves under the direction of President-elect Salvador Nasralla" and cease operations against the election protests.
Former Bolivian President Jorge Quiroga, head of the OAS election observers mission, read a statement to journalists saying the mission "believes it has observed a process of low quality.
OAS Secretary General Luis Almagro said via Twitter shortly before the announcement that election observers concluded "serious doubts persist about the results."
The first results reported by the electoral court before dawn the day after the Nov. 26 election showed Nasralla with a significant lead over Hernandez with nearly 60 percent of the vote counted.
Then public updates of the count mysteriously stopped for more than a day, and when they resumed, that lead steadily eroded and ultimately reversed in Hernandez's favour.
Hernandez, a 49-year-old businessman and former lawmaker, took office in January 2014 and built support largely on a drop in violence in this impoverished Central American country.
But corruption and drug trafficking allegations cast a shadow over his government, and his re-election bid fueled charges that his National Party was seeking to entrench itself in power by getting a court ruling allowing him to seek a second term.
"The people say: 'JOH you are not our President,'" Zelaya tweeted, referring to Hernandez's initials. "We must mobilize immediately to all public places. They are violating the will of the PEOPLE.
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