Mr Fabre, who gained 35%, told AFP news agency the results were a “crime against national sovereignty”.
Observers from the African Union said the election was free and fair.
Mr Fabre’s party, the opposition Combat for Political Change (Cap 2015), said the results bore “no resemblance to those compiled from reports collected in polling stations by its representatives”.
West African regional leaders led by Ghana’s President John Dramani Mahama have been attempting to mediate the dispute, having arrived in the capital Lome on Tuesday.
President Faure Gnassingbe’s family has ruled Togo for 48 years.
Mr Gnassingbe has ruled since the 2005 death of his father, Gnassingbe Eyadema.
On Monday Mr Fabre called for a delay in announcing the results, citing widespread irregularities.
The final results still need to be confirmed by the country’s Constitutional Court.
Turnout was around 53-55%, according to Ceni – at least 10% lower than the last elections in 2010.
The 2005 elections were overshadowed by fraud allegations and violent protests which left at least 400 people dead.
Last year, opposition protests failed to bring about constitutional changes limiting the president to two terms in office – a move that would have prevented Mr Gnassingbe from standing.
Togo’s GDP has more than doubled since 2005 and economic growth reached 5.6% in 2014.
But critics say the benefits have mainly gone to a wealthy minority, while most ordinary Togolese still suffer from high poverty and unemployment rates.