In announcing the 15 trillion won programme - which follows a central bank interest rate cut to a record low this month - the finance ministry also slashed its growth outlook for this year.
Finance Minister Choi Kyung-Hwan said the extra move was crucial as a recovery in Asia's fourth largest economy hinged on efforts to quickly contain the effects of Middle East Respiratory Syndrome.
As of today the virus had killed 29 people and infected 151 since the first case was confirmed on May 20, making it the worst outbreak outside Saudi Arabia.
"The economy is being weighed down by MERS, which has seriously hurt consumption and the service sector," he said, adding the government would use all available resources to prop up growth, support exports and create jobs.
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Choi said the government would issue bonds to fund the extra budget, the size of which will be decided after analysing the impact of MERS.
The finance ministry slashed its growth forecast for this year to 3.1 per cent from an earlier projection of 3.8 per cent.
The slowing global economic recovery and a weak yen and euro are other risks to South Korea, it said.
As part of the package provincial authorities will be encouraged to spend more on infrastructure projects, while it will also be used to help contain MERS, address the effects of a severe drought and create more jobs.
"We're trying to cope with shocks from non-economic issues by boosting fiscal spending sufficiently and keeping it expansionary," said Lee Chan Woo, a director general at the ministry.