Iotova, backed by the ruling centre-left party Progressive Bulgaria, led with about 51 per cent versus 43 per cent to 45 per cent for former caretaker prime minister Andrey Gyurov, according to two exit polls published as voting ended at 8pm on Sunday (5am Monday AEST).
Gyurov is backed by the liberal-conservative opposition camp, signalled closer alignment with Western partners during the campaign, along with stronger support for Ukraine in the face of Russia's full-scale invasion.
The final official result is expected on Monday as the ballots are counted.
The exit polls put voter participation at about 27 per cent to 29 per cent, a bit higher than the first-round race on October 25, which had a record-low turnout of 23 per cent.
The election in the EU and NATO member country on the eastern flank of both blocs is overshadowed by the war in Ukraine. The Black Sea, which Bulgaria borders, is increasingly becoming a theatre of war because of drone attacks on merchant ships, which have sparked international condemnation and concerns about the growing reach of the war.
About two dozen seafarers are feared dead, and the strikes have prompted the government to seek allied assistance to bolster maritime security. On Wednesday, a Greek container ship sank after being hit by sea drones.
Both leading presidential candidates have condemned the attacks.
Prime Minister Rumen Radev, who backs Iotova, said the strikes' outcome "benefits the Russian Federation". The two candidates have both called for a diplomatic end to the war.
Iotova became acting president in January after Radev resigned to enter - and win - a parliamentary race on what many political analysts considered a Kremlin-friendly ticket.
"I voted for Bulgaria to be a strong state in a strong Europe, but for Bulgaria to have its own foreign policy and a voice when it needs to stand up for what matters most - the national interest," Iotova said on Sunday.
Gyurov, who served as caretaker prime minister this year, is supported by pro-Western, reformist parties.
"Today I voted for a secure, stable and European Bulgaria," he said after voting.
He signed a security co-operation agreement with Kyiv during his time as premier.
A host of right-leaning political figures, among them ex-premier Boyko Borissov, have expressed support for Gyurov.
with dpa
