The opposition candidate for mayor of Istanbul has declared victory in a high-stakes repeat election after his rival backed by Turkey's president conceded defeat.

Ekrem Imamoglu's victory means Turkey's largest city won't be governed by President Recep Tayyip Erdogan's party or its predecessor for the first time in 25 years.

Unofficial returns after most votes from Sunday's repeat election were counted showed Imamoglu had a clear majority. His government-backed opponent, former Prime Minister Binali Yildirim, conceded moments after early returns showed him trailing with 44% of the vote to his opponent's 54%.

Speaking to jubilant supporters on Sunday night, Imamoglu said: "Thank you, Istanbul!"

Imamoglu had narrowly won a previous mayoral election on March 31, but Turkey's electoral board annulled the results after weeks of partial recounts.