The two allies signed the military agreement on Friday in a move likely to fuel fresh outrage in Pyongyang which has spent the past few weeks denouncing joint South Korea-US military exercises.
While existing agreements provide for US engagement in the event of a full-scale conflict, the new protocol addresses the response to a low-level action such as a limited cross-border incursion.
It guarantees US support for any South Korean retaliation and allows Seoul to request any additional US military force it deems necessary.
"This allows both nations to jointly respond to the North's local provocations, with the South taking the lead and the US in support," defence ministry spokesman Kim Min-Seok said.
"It will have the effect of preventing the North from daring to provoke us," Kim told reporters.
The United States has close to 30,000 troops stationed in South Korea with the option to bring in reinforcements from its military bases in Japan.
The "provocative" scenarios envisaged by the new pact include maritime border incursions, shelling of border islands, and infiltration by low-flying fighter jets or by special forces units.
The chairman of the South's Joint Chiefs of Staff, General Jung Seung-Jo, said the accord would allow a "strong retaliation" that would make North Korea "bitterly regret" any provocative move.
The protocol was signed just days before the third anniversary of the 2010 sinking of the South Korean naval corvette, Cheonan, with the loss of 46 lives.
South Korea said it was sunk by a North Korean torpedo, although Pyongyang had always denied any involvement.
Later the same year, North Korea shelled the South Korean border island of Yeonpyeong, killing four people.
Angered by UN sanctions imposed after its nuclear test in February, North Korea has issued a wave of threats over the past month -- ranging from a surgical military strike to nuclear war.
The North's young leader Kim Jong-Un recently made a series of visits to frontline military units across the country, during which he threatened to "wipe out" South Korean military units on another border island.
South Korea on Monday held a naval exercise involving combat corvettes and missile patrol ships close to the disputed maritime border to mark the Cheonan sinking anniversary.
The de-facto maritime boundary -- the Northern Limit Line -- is not recognised by Pyongyang, which argues it was unilaterally drawn by the US-led United Nations forces after the 1950-53 Korean War.
It was the scene of deadly naval clashes in 1999, 2002 and 2009.
On Tuesday, President Park Geun-Hye and top military officials will attend a memorial ceremony at the national cemetery in Daejeon, where the victims of the Cheonan sinking are buried.
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