According to unofficial results, Imamoglu received 54.03% of the votes while his opponent, People's Alliance candidate Justice and Development Party's (AK Party) Binali Yıldırım received 45.09% as 99.37 percent of the ballot boxes were counted.
The vote difference between the two candidates was 777,581, significantly higher than 13,729 announced after March 31 elections. Imamoglu led the race in 28 out of Istanbul's 39 districts, greatly improving from 16 in canceled elections.
Soon after the results started coming in, Yıldırım conceded defeat and said his rival Imamoglu was leading the race, congratulating him for the apparent victory.
"We'll try to help out Imamoglu in everything he will do to the benefit of Istanbulites," Yıldırım said.
Speaking shortly after Yıldırım's speech, Imamoglu said the results were crucial for Turkey's democracy.
"Today, 16 million Istanbulites have renewed our faith in democracy, trust in justice. This was realized not only by those who voted for me, but all our citizens who helped us carry this election with great maturity and calm," he said.
Imamoglu also called on President Recep Tayyip Erdogan that he is willing to meet with him as soon as possible.
"I am calling on our head of state, President Erdogan, I'm ready and willing to work in harmony with you on Istanbul's urgent issues such as earthquake safety in the city, subway construction, refugees and so on," he added.
Polling started on Sunday for Turkey’s re-run local elections to elect a new mayor for Istanbul.
Voting started at 8.00 a.m local time (0500GMT) and will continue through 5.00 p.m. local time (1400GMT) in 31,342 ballot boxes across 39 districts of Istanbul.
Ekrem Imamoglu, candidate of the opposition Republican People's Party (CHP), and Binali Yildirim of the ruling Justice and Development (AK) Party, will vie to run the metropolitan municipality of Turkey's most populous city after a previous vote on March 31 was annulled by the country's top election council last month.
Millions of Turkish voters cast their votes nationwide on March 31 in local elections to choose mayors, city council members, mukhtars (neighborhood officials), and members of elder councils for the next five years.
On March 31, the turnout was 83.88%, six percentage points lower than the previous local elections of March 30, 2014.
In Istanbul, Imamoglu received 48.8% of the vote, whereas Yildirim got 48.55%, according to official figures from the Supreme Election Council (YSK).
AK Party won 24 district municipalities across the province, while the CHP won 14.
The results in March were canceled after AK Party and its coalition partner, the Nationalist Movement Party (MHP), appealed to the YSK, citing irregularities and contradictions with legal measures, leading to the annulment of Imamoglu's mayoral certificate.
YSK chief Sadi Guven said all eligible voters who cast their ballots in the March 31 poll would be able to do so again in a re-do vote for Istanbul’s metropolitan mayor.
However, 44,852 voters were removed from the electoral lists due to conviction, military service or death.
The YSK announced the total number of voters would be 10,560,963 for the June 23 elections.
On the March 31 elections, voters chose from among 32 candidates -- 24 of them independent -- on the ballot.
This time, there will be only 21 candidates, including nominees from AK Party, the CHP, the Felicity (Saadet) Party and the Patriotic (Vatan) Party along with 17 independent hopefuls.
- Why re-run elections?
The YSK ruled in favor of a re-run, with seven votes in favor and four against.
Some 30,281 votes in 108 ballot boxes were declared invalid due to vote-counting sheets being unsigned or absent altogether, the country's Supreme Election Council (YSK) said in a statement.
Also, polling clerks who were not civil servants served in 754 polling centers in the March 31 mayoral elections in Istanbul.
The council said this practice was unprecedented and influenced the difference between the ruling and opposition alliances -- down to 13,729 ballots -- and therefore raised questions on the validity of results.