An official winner of the November 26 election has still not been announced, and the small Central American nation of 10 million has been mired in uncertainty since the vote.
"The result is consistent" with that which previously put Hernandez ahead by 1.6 percent, David Matamoros, the president of the tribunal, said following the recount of 4,753 ballot boxes.
An initial count following the election put challenger Salvador Nasralla comfortably ahead of the incumbent, but the tribunal later gave Hernandez the advantage.
Nasralla, a 64-year-old former TV presenter with minimal political experience, insists the vote was "rigged" to deny him a clear victory.
International observers have expressed reservations over the poll, which the Organization for American States said was marred by irregularities.
Supporters of both candidates have held demonstrations and sporadic violence has occurred.
"I'm out here marching because I want my vote to be respected. Im the one who is supposed to decide, not the people who have always been in charge," said clothes retailer Anonia Vasquez, 51.
"The people here said no to reelection. And the president is giving a bad example," she argued.
Amnesty International denounced "dangerous and illegal tactics" to silence dissent.
It said at least 14 people have been killed since the election, but there was no confirmation from police or other officials of that toll, at least in relation to the political crisis. The death of one young woman and two officers have been confirmed.
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