Sadi Guven on Monday described the elections, in which President Recep Tayyip Erdogan won a new five-year term with vastly increased powers, as "healthy" and said the results would be opened for public scrutiny in 10 days.
Speaking early on Monday, Supreme Election Council head Sadi Guven said 97.7% of votes had been counted and declared Mr Erdogan the victor.
However the opposition raised doubts about the accuracy and reliability of the figures released by state-run Anadolu news agency, the sole distributor of the official vote tally.
His main rival Muharrem Ince of the Republican People's Party (CHP), who had challenged Erdogan with an energetic campaign, broke an uncharacteristic overnight silence to declare on Monday he accepted the results.
In his final campaign rally in Istanbul on Saturday, Mr Ince urged his CHP supporters to head to polling stations and carefully monitor ballot boxes to prevent election fraud.
Worldwide observers have denounced the lack of "equal" conditions for candidates to campaign in Turkey's twin presidential and parliamentary elections that were swept by incumbent President Recep Tayyip Erdogan and his ruling party.
Western leaders have been slow to congratulate Erdogan on his election victory, but Russian President said his electoral victory gave him "great political authority and mass support".
The nation has entrusted me the role of president and executive power.
The president has arrested and jailed many of his opponents and critics since the attempted coup in 2016.
The main opposition CHP will have 146 seats, the pro-Kurdish HDP 67 and the breakaway nationalist Iyi Party 44.
Erdogan is now Turkey's first president under the new presidential system of government, which was chosen by Turkish voters in an April 2017 referendum. Under a new constitution agreed in an April 2017 referendum strongly backed by Erdogan the President can exclusively take a decision without even a prime minister's approval.
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Last night, Erdogan was already celebrating the "victory of democracy" in a short speech while in downtown Istanbul his supporters were hailing Allah from vehicle carousels.
But Mr Erdogan - who has been in power since 2003 - faced a more robust and united opposition, which vowed to return Turkey to a parliamentary democracy with strong checks and balances.
Conceding defeat, Ince warned that constitutional changes ushered in by Erdogan earlier in the year represented a threat to the country's democracy. With virtually all votes counted, Erdogan had 53 per cent against Ince's 31 per cent, while in the parliamentary vote the AKP took 42.5 per cent and its MHP nationalist allies secured 11 per cent, outstripping expectations.
Also Monday, Kosovo President Hashim Thaci congratulated Erdogan in a tweet, adding: "Looking forward to our continued good cooperation".
Mr Erdogan said there had been no serious voting violations.
Previously divided opposition parties have come together in a tenuous alliance in an effort to end what they call Erdogan's march toward "one-man rule".