The former Kyrgyz prime minister will become president after opposition leader Omurbek Babanov conceded defeat after Sunday's poll.
Sooronbai Jeenbekov, a protege of the outgoing president, won Sunday's vote with 55 percent – a stronger result than the near tie polls had predicted.
Opposition leader Omurbek Babanov on Monday conceded defeat but said he would investigate irregularities.
The election was seen as a test of stability in the central Asian country where Russia still holds considerable sway and two previous leaders were ousted in violent riots.
The vote was competitive and candidates could, in general, campaign freely, the Organisation for Security and Cooperation in Europe (OSCE) said.
But cases of misuse of public resources, pressure on voters and vote-buying remained a concern, it added.
The election "contributed to the strengthening of democratic institutions by providing for an orderly transfer of power," the mission's statement said.
An official confirmation of the figures is expected within a week. An unchallenged result would mark the first peaceful transition of power between full-time presidents in the mostly Muslim nation.
Pre-election polls had suggested both candidates would fail to get 50 percent and have to proceed to a second-round runoff.
Both candidates differed little on the main points of policy during the campaign: a secular state and hewing close to Russia in a region where Moscow vies for influence with the United States and China.
However, they represent rival interest groups and clans inside Kyrgyzstan that are fighting for access to power and state resources.
Outgoing President Almazbek Atambayev, who has developed especially close ties with Moscow during his six years in office and stepped down because of term limits, is likely to remain a powerful figure.
Atambayev and Jeenbekov's Social Democratic party has the biggest faction in parliament and dominates the coalition cabinet. Jeenbekov has pledged to continue his predecessor's policies.
Kyrgyzstan hosts a Russian military base.