However, hours later, the Organization of American States (OAS) said the process did not meet democratic standards and called for a fresh election.
Fueling the confusion, European Union observers on Sunday said the vote recount showed no irregularities.
Furious that Hernandez had been declared winner, protesters clashed with police in the capital Tegucigalpa, blocked roads around the Central American country's main port, and partially burned a courthouse and bank branch in San Pedro Sula, Honduras's second biggest city.
"We are not going to stop protesting, we are not going to let them steal the elections from Salvador Nasralla or keep Juan Orlando Hernandez in power," said Antonio Tejada, 30, his face covered with a red bandana in the center of the capital.
Nearby, military police cleared rocks and burning tires from the streets.
Nasralla, a former TV host Salvador, leads a center-left coalition that seemed headed for a surprise upset in the hours after the Nov. 26 election, before results suddenly stopped coming in. When they restarted, the outcome began to favor the incumbent.
Honduras has been roiled by political instability and violent protests since then. The count has been questioned by the two main opposition parties, including the Opposition Alliance Against the Dictatorship, headed by Nasralla, as well as a wide swath of the diplomatic corps.
The OAS report described irregularities - including deliberate human intrusions in the electoral computer system, pouches of votes opened or lacking votes, and "extreme" improbability around voting patterns it analyzed - making it "impossible to determine with the necessary certainty the winner."
Former Honduran President Manuel Zelaya, who supports Nasralla, said on Monday the protesters should not back down.
However, Zelaya, who was ousted in a coup in 2009, said the Alliance was ready to accept new elections if Nasralla, who was meeting U.S. and OAS officials in Washington on Monday, agrees.
"We would accept that to guarantee peace," Zelaya said on a television show. "The Honduran people don't want war, we don't want war."
Honduras's chaotic election marks the start of a voting season in Latin America that will see more than two-thirds of the region's population electing new leaders over the next 12 months.