The Islamic republic's supreme leader Ayatollah Ali Khamenei, who has final say in all state matters, cast his ballot when the polls opened at 08:00 am (0430 GMT), state TV showed.
"We are starting the second round of the 14th presidential election to choose the future president from among the two candidates across 58,638 polling stations in the country and all stations abroad," Interior Minister Ahmad Vahidi said, according to state TV.
In last week's first round, Pezeshkian, who was the only reformist permitted to stand, won the largest number of ballots, around 42 percent, while the former nuclear negotiator Jalili came in second place with 39 percent, according to figures from Iran's elections authority.
Only 40 percent of Iran's 61 million eligible voters cast their ballot, the lowest turnout in any presidential election since 1979.
On Wednesday, Khamenei called for a higher turnout in the runoff.
"The second round of the presidential election is very important," he said in a video carried by state TV.
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