The election was delayed to allow experts to clean up the voter roll, which opposition parties said was full of inaccuracies that might favor the president.
"If they insist on using (the electronic system), this could lead to a popular uprising," said Eric Dupuy, a spokesman for Fabre.
There was no immediate comment from the election commission late on Friday.
A spokesman for the U.N. Secretary-General appealed for any challenges to be made in the courts, not on the streets.
Faure Gnassingbe is seeking a third term in power. He is facing a divided opposition and controversy over how results are tallied and announced. Gnassingbe has been president since 2005 when his father died after 38 years in charge. Campaigning has been largely peaceful and there are no signs of the tensions that led to violence in 2005, when hundreds died after the election.
Results from the single round of voting could start to flow in on Sunday. However, it has been delayed for 10 days by the row over the counting procedure and, with the risk of results being challenged, diplomats issued last-minute appeals for calm.
Togo's constitution allows three terms in office, unlike Democratic Republic of Congo, where efforts to change laws to allow the president to seek a third term have led to violent protests. A bid to change the constitution for the same reason in Burkina Faso last year led to the overthrow of the president.
"I am convinced that my voice will count toward a certain change in this country. It's my dearest wish," said Afi Amegnon, 36, at a polling station in the capital.
Gnassingbe has pledged to ease poverty by pursuing the infrastructure-driven economic growth he has overseen since the 2005 violence.
Campaign slogans, dominated by puns using his first name, Faure, and the French for "strong", pledge more schools, roads and opportunities in the transport and services hub he is trying to establish in the nation of 7 million.
However, after 48 years with the same family in charge, his rivals say Togo needs new leadership. Strikes by teachers and medics have in recent months turned violent.