Opposition candidate Felix Tshisekedi was provisionally declared elected president by the country's electoral commission in the early hours of Thursday morning.
Tshisekedi received more than seven million votes, compared to about 6.4 million for Fayulu, who had warned against manipulation.
Mr Shadary received more than 4 million votes.
The Tshisekedi's victory is deeply controversial as pre-election polls had given outspoken opposition frontrunner Martin Fayulu, a respected former business executive, a healthy lead.
A CENI source and a diplomat said they expected results to be announced later on Wednesday.
While Nshole acknowledged the difficulties in manually counting votes, especially in remote areas, he warned that the longer the election results are delayed, the more that suspicion will grow among the Congolese people.
Tshisekedi's father, Etienne, was a famous opposition leader under Mobutu. I ask the Cenco, the Church of Christ in Congo, the Symocel and all those who observed the elections to tell us the truth, to publish the results.
Kabila has ruled since 2001 in the troubled nation rich in the minerals key to smartphones around the world. The electoral commission said this was due to an Ebola outbreak and violence there, but it means about a million people have been disenfranchised because the new president is due to be sworn in this month.
Shortly after the results were announced, Tshisekedi paid his respects to outgoing President Joseph Kabila, describing him as "an important political partner".
Congo's powerful Catholic Church has upped the stakes by saying it found a clear victor from data compiled by its 40,000 observers deployed to all polling stations. "The United States, SADC, and the European Union should respond strongly with sanctions if that occurs", he added.
Fayulu, who was running well ahead of Tshisekedi in opinion polls ahead of the election, on Thursday called on the Congolese people to "rise as one man to protect victory". And in a last-minute decision, some 1 million of the country's 40 million voters were barred from participating, with the electoral commission blaming a deadly Ebola virus outbreak.
Congo's government cut internet service the day after the vote to prevent speculation on social media. The New York Times cited a senior adviser to Kabila as saying the Catholic group believed Fayulu, rather than Tshisekedi, won comfortably.
"These people have negotiated with Kabila so that he can stay in power".
Opposition activists on Wednesday threatened to take to the streets if CENI failed to announce the results.
The 56-year-old Tshisekedi took over as head of Congo's most prominent opposition party in early 2018, a year after his father's death.