The projectiles were fired at 5.24 a.m. and 5.36 a.m. from North Korea's Kwail county in South Hwanghae province, and both flew around 450 km across the peninsula before splashing into the East Sea, Yonhap News Agency quoted the Joint Chiefs of Staff (JCS) as saying.
Their maximum altitude was about 37 km, and the top speed was around Mach 6.9, according to the JCS.
"South Korean and US intelligence authorities believe that these short-range missiles bear similar flight features to the ballistic missiles North Korea test-fired on July 25," the JCS said, adding that analysis was underway to determine their exact type.
"Our military is monitoring the situation in case of additional launches and maintaining a readiness posture."
In a fresh warning after the firing on Tuesday, North Korea's Foreign Ministry said that it could seek "a new road", other than engagement, calling the joint exercise a violation of a series of joint agreements they signed with the North.
"The US and South Korean authorities remain outwardly talkative about dialogue. But when they sit back, they sharpen a sword to do us harm," the Ministry said, according to the North's Korean Central News Agency.
"If the US and South Korean authorities trust to luck, disregarding our repeated warnings, we will make them pay heavy price which will in turn make them very much difficult," it added.
Meanwhile, South Korea's presidential office Cheong Wa Dae held an emergency meeting to discuss the latest launch, Yonhap news agency quoted spokesperson Ko Min-jung as saying.
"We see the launches as a violation of the spirit of the inter-Korean military agreement," defense ministry spokesperson Choi Hyun-soo told a regular briefing, referring to the Comprehensive Military Agreement signed in September last year.
In Washington, a senior US official told Yonhap that it was continuing to monitor the situation.
This is the fourth such launch in less than two weeks.
The first recent launch took place on July 25 when the North fired two rounds of a new type of ballistic missile for the first time in 77 days.
The country then conducted additional launches on July 31 and August 2.
( With inputs from IANS )