The insurgents have threatened to target polling stations on Saturday when voters will choose between former foreign minister Abdullah Abdullah and ex-World Bank economist Ashraf Ghani.
The second-round vote on Saturday comes as US-led NATO troops withdraw after more than a decade of fighting the Taliban, who were ousted from power in 2001 for sheltering al Qaeda militants behind the 9/11 attacks.
Afghan officials are desperate to repeat the success of the first-round vote in April, when the insurgents failed to launch a single high-profile attack as long lines of voters turned up across the country to cast their ballots.
"We hope our security measures will be even better than the last election," General Sher Mohammad Karimi, the army's chief of staff, told reporters in Kabul.
"We have very good planning and coordination with our security forces, and they are on the highest state of alert... The enemy suffered a heavy blow last time, so they have vowed to disrupt the run-off."
Outgoing President Hamid Karzai has also ordered all security personnel to remain neutral in Saturday's election, as officials try to avoid the massive fraud that undermined the 2009 poll when he retained power.
Abdullah secured 45 per cent of the first-round vote, with Ghani on 31.6 per cent, according to the final results, which came after weeks of deliberation over fraud allegations.
They were the two leading candidates in an eight-man field, triggering the run-off election as neither reached the 50 per cent threshold needed for outright victory.
General Mohammad Zahir Azimi, the ministry of defence spokesperson, said about 400,000 soldiers, police and intelligence forces were involved in the election security plan.
Nations that have fought in Afghanistan and donated billions of dollars in aid since 2001 see a smooth transition of power as a key benchmark of success, despite continuing violence.
A suicide attack targeting Abdullah last week killed 12 people, though he was left unharmed.
Karzai, who is constitutionally barred from a third term, has ruled since the end of the austere Taliban era, when men were beaten for not having beards and women were forced to wear the all-enveloping burqa.
The Taliban in a statement warned Afghans to "remain far away from the polling stations... lest you should be hurt or killed."
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Alas... I hope and pray for peace in Afghanistan in my lifetime.. I hope and pray that the situation like Iraq does not occur here..