On Sunday, Nasralla supporters in the capital of Tegucigalpa marched near to where the count was resumed, banging on pots...
"We have now finished this recount," Supreme Electoral Tribunal president David Matamoros said, announcing that Hernandez had 42.98 percent of the vote compared with opposition leader Salvador Nasralla's 41.39 percent.
He added that the body could take up to 22 days to declare an official winner because of possible appeals.
"We urge all candidates and all parties to put Honduras first," Matamoros said.
On Sunday, Nasralla supporters in the capital of Tegucigalpa marched near to where the count was resumed, banging on pots, blaring vuvuzelas and singing campaign songs which included insults towards Hernandez.
"They are stealing our votes," a visibly angry Jesus Elviz, a 58-year-old accountant, told AFP.
On Friday, 19-year-old Kimberly Fonseca was killed by a bullet during a confrontation between protesters and the police. Her family says she was killed by police, a claim the authorities said they were "exhaustively" investigating.
After the violent protests erupted -- with some reports of looting -- the government declared a state of emergency and imposed a 10-day curfew in an attempt to curb the unrest.
Hernandez's conservative National Party -- which controls the executive, legislative and judicial branches of government -- is constitutionally barred from a second term, but it contends that a 2015 Supreme Court ruling allows his re-election.
Nasralla and his leftist coalition, the Opposition Alliance Against the Dictatorship, have denounced the incumbent's bid as illegal.
Situated in the heart of Central America's "Northern Triangle," where gangs and poverty are rife, Honduras has one of the highest murder rates in the world -- though it has fallen under Hernandez.
What credit he claims from that progress, however, is counterbalanced by tensions over his re-election bid.
It is a loaded issue in Honduras, where former president Manuel Zelaya was toppled in a coup in 2009 -- notably because he was accused of plotting to change the constitution to stand for a second term.