The outcome of the vote is too close to call, with voters given a choice between moderate cleric Akbar Hashemi Rafsanjani and ultra-conservative Tehran mayor Mahmood Ahmadinejad.
Hundreds of supporters from both sides debated fiercely, but peacefully, in squares throughout Tehran on Wednesday evening.
Mr Ahmadinejad backers handed out flowers while their rivals fans waved banners.
The election, billed as the most crucial elections in the Islamic republic’s history, has exposed deep class divisions in Iranian society and sparked heated rows among the Islamic state’s top clerics.
It’s pitting a moderate conservative vowing to improve ties with the West against a man who espouses the “purity” of the revolution and many fear will roll back cautious social and economic reform.
Its outcome will likely determine whether outgoing President Mohammad Khatami’s cautious domestic reforms and foreign policy of detente continue or grind to a halt.
Mr Rafsanjani must win over the support of disenchanted reformers and an apathetic electorate if he is to win. A loss would leave all Iranian institutions in the hands of the anti-Western right.
It could also see Iran adopting a less conciliatory foreign policy, something that has already worried governments in Europe involved in delicate negotiations with Tehran over its nuclear programme.
As allegations of foul play and an orchestrated election plot continue to swirl, Mr Rafsanjani’s persuaded a series of high-profile supporters to line up to denounce his opponent.
But Mr Ahmadinejad’s camp has been busy trying to shake off the “extremist” tag plastered on their candidate since his shock success in last week’s first round.
He said talk he was an Iranian “Taliban” were “lies on a grand scale”.
Tensions have intensified by allegations of dirty tricks in the first round and fears they could be repeated in the second.
Mr Rafsanjani has managed to mobilise broad support from reformist and conservative groups but it remains to be seen whether disillusioned liberals will line up behind the 70-year-old ayatollah.
His biggest threat is perhaps a substantial boycott of the vote by liberals who argue the whole process is flawed, given that all the candidates were chosen by the ultra-conservative Guardians Council in the first place.
Mr Ahmadinejad, 48, has gained momentum as a populist public servant in touch with key issues such as unemployment, housing, purchasing power and economic corruption.
But as an ultra-conservative who spoken out against “uncontrolled” cultural policies and “decadence”, he is a less palatable prospect for Iran’s centre and left.