The electoral commission’s declaration came as Mr. Nasralla was on his way to Washington to meet with the Organization of American States and the State Department.
In a video posted on his Facebook page from the airport in Miami, Mr. Nasralla said, “The fight continues and will continue.” He said the result announced by the commission “has no validity simply because the Organization of American States, of which Honduras is a member, does not endorse the results.”
In a sign that Mr. Hernández was prepared to challenge O.A.S. directly, the president’s top adviser, Ebal Diaz, accused Mr. Almagro of violating the observation mission’s protocols and of “generating more violence.”
“You have been irresponsible, allowing a member of your team to scheme with” Mr. Nasralla “to try and steal the election,” wrote Mr. Diaz, the executive secretary of the president’s council of ministers.
On Friday, a national strike led to clashes between protesters and the military police at roadblocks around the country. At least 22 people have been killed since the disputed vote, according to the Committee of Relatives of the Disappeared in Honduras, a human rights group.
Preliminary results on election night suggested that Mr. Nasralla had a strong lead, but the count was then stopped for more than a day. When the counting resumed, Mr. Hernández was reported to have begun closing the gap as new results were registered. Eventually, the electoral commission’s tally gave him a small lead.
Election observers from the O.A.S. said on Dec. 6 that the “irregularities, mistakes and systemic problems plaguing this election make it difficult” to be “certain about the outcome.”
The organization backed a call for a partial recount, and the electoral commission went ahead with the tally. The alliance of leftist parties backing Mr. Nasralla, as well as a third party, the Liberal Party, handed over their copies of the tally sheets from polling places to the O.A.S. and asked for the results to be nullified.
On Sunday, Mr. Matamoros, the electoral commission president, said in a brief televised statement that the agency had complied with all the O.A.S. recommendations.
Election observers from the European Union said Sunday that the opposition had failed to show a significant difference between their copies of the tally sheets and those that were counted by the electoral tribunal. But the group said the tribunal and the Honduran Supreme Court should consider any additional appeals.
The election result creates a dilemma for the Trump administration, which has pressed in public for a transparent vote count but said nothing about irregularities.
Two days after the election, the State Department certified that the Honduran government was making progress on improving human rights and tackling widespread corruption — a sign of support for Mr. Hernández. The Honduran president has proved to be a strong ally on the issues that matter most to the United States, interdicting drugs and dissuading migrants from making the long trip to the Texas border.
But that alliance could prove uncomfortable if Mr. Hernández begins his second term in January with his legitimacy under a cloud. Although Congress has supported aid to Honduras, legislators have already raised concern over the disputed vote count.
Senator Patrick J. Leahy, who has held up delivery of some aid to the Honduran government over concerns about human rights, said Sunday that the election result “leaves too many questions unanswered.
“There were multiple opportunities for fraud in this election, and only a determination by impartial international observers that the vote tally was fair and transparent will provide the necessary credibility to the process,” he said in an emailed statement.
Mr. Leahy also called on the government to stop shooting at protesters. “There is no justification for the tragic loss of life that has occurred,” he wrote.
Mr. Nasralla’s alliance has called for protests on Monday. The Liberal party has scheduled protests for Tuesday.
An earlier version of this article gave the wrong date for the Honduran election. It was held Nov. 26, not Nov. 27.