The partial results of the elections, announced earlier by CENI, said Gnassingbe, son of Gnassingbe Eyadema, who led Togo for 38 years, was in the lead, but both candidates claimed victory.
At least 3.2 million Togolese were eligible to vote in Thursday's election, seen as a key test of the country's resolve to turn a page on electoral bloodletting.
"All the results we have confirm that President Faure has resoundingly, I mean resoundingly, won this election," Pascal Bodjona, a government spokesman, told Radio France Internationale on Friday.
Earlier that day, Fabre, a deputy in Togo's parliament and candidate of the opposition Union of Forces for Change (UFC), also said he had won.
"On the basis of the counts from certain prefectures, the UFC candidate has won an average of 75 to 80 per cent of the votes," he said in an address to party supporters.
"We conclude that we have won the presidential election of March 4, 2010."
Call for calm
Their competing claims came after election officials called on citizens to remain calm while results from Thursday's poll are tallied.
In a statement broadcast on state television, the independent electoral commission urged candidates and voters to "exercise patience and serenity while the commission makes every effort to centralize the results from various polling stations".
The race pitted six opposition candidates against Gnassingbe, 43, who came to power in 2005 after the death of his father, General Gnassingbe Eyadema, whose dictatorial rule lasted 38 years.
Gnassingbe, a former mines minister and financial adviser under his father, is seeking a second-term mandate but the opposition dismisses him as a candidate of "a system" that froze development over the past 43 years.
Gnassingbe vowed that this poll will raise Togo to new heights, on the basis of "a state of law".
Voting deemed 'peaceful'
With the main opposition party expressing concern over possible electoral fraud, 40 international observers were deployed by the African Union, 130 by the European Union and 150 civilians and 146 soldiers by the Economic Community of West African States (Ecowas) to oversee the elections.
The commission had vowed to stage a free and fair poll, devoid of violence, and observers agreed the voting was peaceful.
Election officials were trying to prevent a situation similar to Togo's presidential election in 2005 when hundreds of people died in post-election violence.
The violence that followed the disputed vote in 2005 left up to 800 dead according to various sources, but the UN put the toll at 400 to 500 deaths.
Yet parliamentary elections two years later were peaceful, raising hopes of an end to Togo's long history of political violence and leading to the restoration of foreign aid.