The message from the Korean People's Army general staff was delivered through an inter-Korean military hotline, the ministry said in a statement.
The 48-hour period will expire at 5:00pm (0800) on Saturday.
The warning was delivered after North Korea fired a rocket across the border, prompting South Korea artillery units to retaliate with dozens of 155mm howitzer shells.
Cross-border tensions have been elevated for weeks following mine blasts that maimed two members of a South Korean border patrol earlier this month and the launch Monday of a major South Korea-US military exercise that infuriated Pyongyang.
