As reported at 13:00UTC by Reuters, official verified results reported by the Nation media group showed Ruto taking 51% of the vote, ahead of left-leaning opposition leader Raila Odinga who had 48%.
A Reuters tally of 255 out of 291 preliminary constituency-level results at 12:00UTC on Sunday showed Ruto in the lead with 52% and Odinga at just over 47%. Two minor candidates shared less than a percent between them.
Minutes before 13:00UTC, Agence France-Presse's tally had Deputy President William Ruto holding 51.25 percent of the vote, reversing earlier gains for his main rival Raila Odinga, who now had 48.09 percent, according to data from the election commission covering nearly 50 percent of constituencies.
The preliminary tally is based on forms that are subject to revision if any discrepancies are discovered during the official verification process.
Ruto's showing, according to observers, reflects widespread discontent with Incumbent President Uhuru Kenyatta's legacy - even in parts of the country where the president has previously swept the vote. Kenyatta had thrown his support to Odinga.
Large numbers of Kenyans also did not vote, saying neither candidate inspired them.
The fracas prompting deployment of security to the counting center, known as Bomas, underscored fraying tempers and high tensions within the national counting hall as the country waits for official results from last Tuesday's election.
As the tight race continued, party agents have grown increasingly agitated at the tallying center. Late on Saturday, Raila Odinga's chief agent Saitabao ole Kanchory grabbed a microphone and announced "Bomas of Kenya is a scene of crime," before officials switched off his microphone.
More than a dozen civil society groups, trade unions as well as the Kenyan chapters of Amnesty International and Transparency International issued a statement Sunday urging calm.
"We call on all political candidates, their supporters and the public to exercise restraint. We must all avoid raising tensions that could easily trigger violence," the group of 14 organizations said.
Both candidates have pledged to maintain calm, with the memory of the 2007-08 and 2017 post-poll violence still fresh for many Kenyans.
At a church service in Nairobi on Sunday, Odinga, 77, recited the opening lines of the Peace Prayer of St Francis and said: "I want to become an instrument to bring peace, to heal, to unite and keep the hope alive in our country."
On Sunday, Ruto's party member Johnson Sakaja won the governorship of the capital Nairobi, the wealthiest and most populous of the 47 counties.
The election is being closely watched by an international community that views Kenya as a pillar of stability in a volatile region, with US Secretary of State Antony Blinken describing the country's polls "as a model for the continent".
"We encourage peace and patience as the vote tallying continues from the August 9 elections," Blinken said on Twitter late Saturday.
The winner of the presidential race needs to secure 50 percent plus one vote and at least a quarter of the votes in 24 of Kenya's 47 counties.
If not, the country will be forced to hold a runoff within 30 days of the original vote.
Observers say that with the race so close, an appeal to the Supreme Court by the losing candidate is almost certain, meaning it could be many weeks before a new president takes office.
This report was compiled with information supplied by Reuters and Agence France-Presse