The launches, which the military said took place around 4 a.m. (1900 GMT), come as relations between the two Koreas are at one of their lowest points ever.
"South Korean and U.S. intelligence authorities were analyzing the launches while monitoring signs of additional activities," the JCS said.
North Korea fired two ballistic missiles into the sea on its opposite coast toward Japan just three days earlier.
The recent weapons tests are the latest in a series by Pyongyang and come as Seoul and Washington ramp up defense cooperation in the face of soaring tensions with the North.
Diplomacy between Pyongyang and Seoul has stalled and North Korean leader Kim Jong Un has called for ramping up weapons development, including tactical nukes.
In response, Seoul and Washington have staged joint military exercises with advanced stealth jets and US strategic assets, while an American nuclear-armed submarine this week made a South Korean port call for the first time in decades.
On Thursday, North Korea's defense minister Kang Sun Nam said the Ohio-class submarine's deployment may have fallen "under the conditions of the use of nuclear weapons specified in the DPRK law on the nuclear force policy," using an acronym for North Korea's official name.
A day later, South Korea's defense ministry reiterated that any use of nuclear weapons by the North would prompt an "immediate and decisive response" resulting in the "end" of the Kim regime.
Saturday's incident also comes as a U.S. soldier is believed to be in North Korean custody after breaking away from a tour group visiting the Demilitarized Zone.
The United States has said it is "very concerned" about how Private Second Class Travis King would be treated, and that as of Thursday, Pyongyang had yet to respond to inquiries about the soldier.
King was due to return to the United States to face military discipline after serving jail time in South Korea for assault.