Opposition presidential candidate Martin Fayulu has warned election officials in the Democratic Republic of Congo not to "disguise the truth" as tensions mount over the delayed result. He received more than 7 million of the 18 million votes cast (38 percent), the commission said.
Tshisekedi received more than seven million votes, compared to about 6.4 million for Fayulu, who had warned against manipulation.
Fayulu, who came second in the presidential poll behind Felix Tshisekedi, called the results fraudulent.
Candidates can appeal results if they wish and the final decision will be announced by the constitutional court.
"Felix Tshisekedi is provisionally declared the elected president of the Democratic Republic of Congo", said Corneille Nangaa, the head of the Independent National Election Commission (CENI).
CENCO has yet to make an official announcement about its results, but it is expected to hold a press conference at 12:30 and to prepare a briefing for the UN Security Council which will meet on Friday.
The election may enable Congo to achieve its first peaceful, democratic transfer of power since independence in 1960.
The opposition was weakened by internal arguments and the exclusion by the electoral commission of two political heavyweights: Jean-Pierre Bemba, a former warlord, and Moïse Katumbi, a popular tycoon.
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The country's influential Catholic Church signaled last week that it knew who had won, having gathered data and recorded infringements of election rules on polling day. "The United States, SADC, and the European Union should respond strongly with sanctions if that occurs", he added.
Observers said many polling stations opened late and closed early and in some places voting machines malfunctioned.
Some Congolese tired of Kabila's long rule, two turbulent years of election delays and years of conflict that killed millions of people said they simply wanted peace. The New York Times cited a senior adviser to Kabila as saying the Catholic group believed Fayulu, rather than Tshisekedi, won comfortably.
Opposition activists on Wednesday threatened to take to the streets if CENI failed to announce the results.
Tshisekedi junior took the helm of the party after his father died in February 2017.
Some Congolese have said Tshisekedi lost support by splitting the opposition.
Tshisekedi, who was born in capital Kinshasa, ran on a pledge to fight corruption and poverty.