Nationwide, less than 15 percent of the ballots had been counted from the almost 890,000 registered voters
Counting was slow and there was still little indication of the eventual winner of an election marked by an ongoing internet blackout in the small west African nation.
However, opposition leader Adama Barrow scored a symbolic victory in the capital Banjul, highlighting the strong challenge posed to Jammeh, who is standing for a fifth term.
Barrow took nearly 50 percent of the vote in Banjul's three constituencies, according to the Independent Electoral Commission (IEC).
Jammeh had 43 percent while third party candidate Mama Kandeh took 7.6 percent, the IEC said.
Nationwide, less than 15 percent of the ballots had been counted from the almost 890,000 registered voters.
Before dawn broke, military and police, some covering their faces, set up checkpoints every few hundred metres on the outskirts of the capital, while citizens were inside sleeping or watching the results come in.
Both Barrow and Jammeh said on Thursday they had won by a huge margin.
"Power belongs to the people. You cannot stop us and you cannot stop them," Barrow said.
Jammeh, who once said he would govern for a billion years if God willed it, predicted "the biggest landslide in the history of my elections."
The United States said turnout appeared to be high and that the vote took place in "generally peaceful conditions", while the IEC hailed "a very successful election."
The US State Department and Human Rights Watch voiced concern however over a blanket cut to internet and international phone calls, as well as claims of voter intimidation.
"The government's communications cutoff and threatened protest ban are only likely to increase tensions between the government and opposition groups," said Babatunde Olugboji from Human Rights Watch.
At his final campaign rally, Jammeh warned that protests over the election result would not be tolerated, saying The Gambia "does not allow" demonstrations.
Information Minister Sheriff Bojang said Thursday the shutdown was to stop the spread of "false information" over the results, and described it as a "security measure".
There was a brief resumption of service around 5:00am (0500 GMT), but diplomats believe the shutdown could last until Sunday.
The opposition has relied on messaging applications and texts to organise rallies and move around roadblocks set up in Banjul during the last week of campaigning.
The winner in the three-way race will serve a five-year term in the tiny former British colony with pristine beaches that occupies a narrow sliver of land surrounded by French-speaking Senegal.
Jammeh is running for a fifth term with his ruling Alliance for Patriotic Reorientation and Construction (APRC).
He faces previously unknown businessman Barrow, chosen as the opposition flag bearer by a group of political parties who have joined forces for the first time and won unprecedented popular support.
Third candidate Kandeh is popular among The Gambia's Fula people and is a former ruling party MP running for the Gambia Democratic Congress (GDC).
All three men are 51, born in 1965, the year The Gambia won independence from Britain.
If Barrow were to win -- a tall order both in terms of votes and the likelihood of Jammeh giving up power -- he would likely decide to serve a three-year term at the head of a transition reform government.
No professional international observers were on the ground for the vote, diplomats confirmed, but a small team of African Union experts monitored events along with Banjul-based US and European delegations already present in the country.
A Senegalese security source confirmed to AFP in Dakar that The Gambia had closed the borders on Thursday, a common occurrence during elections in west Africa.
Jammeh seized power in a 1994 coup and has survived multiple attempts to remove him from the presidency.
Some 60 percent of the population live in poverty in The Gambia, and a third survive on $1.25 (1.20 euro) or less a day, according to the UN.