Pictures from the rally show huge crowds filing through the streets of Istanbul towards one of the main squares in the city.
A similar rally occurred in the capital Ankara two weeks ago, showing the increasing divide between secularists and Islamic elements of Turkey's communities.
Abdullah Gul is the ruling party candidate for the election, but he failed to win a first-round victory after a number of MPs boycotted the election and challenged the vote.
A court has said it will try and rule on the appeal decision before the second round of voting which is due to begin on Wednesday.
Turkey's prime minister, Tayyip Erdogan, heads the Islamic-rooted AK party, which is an offshoot of the first Islamist party which was forced from power by the military in 1997.
The AK party denies any wrongdoing in the election wrangling and has said that any action from the military should not occur in a democratic state.
Mr Gul has said he will not quit, despite the growing concern from secularists and the military that he remains loyal to his Islamic roots.
Turkey wants to join the European Union (EU) and the EU has added its voice to the condemnations of any military interference in the diplomatic process.
Talks regarding Turkey's entry into the EU are not currently going forward due to the ongoing dispute with Cyprus and the country's political reform.
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