In an unusual move, President Park Geun-Hye personally observed the test exercise, a defence ministry official said.
"The military tested two home-developed, long-range missiles that could hit any target in North Korea," the official told AFP on condition of anonymity.
The test came almost a month after North Korea said it had successfully tested a submarine-launched ballistic missile (SLBM) -- a claim which numerous experts said was probably exaggerated.
As well as the SLBM test, Pyongyang recently boasted of its ability to miniaturise a nuclear warhead to fit on high-precision, long-range rockets.
Experts also questioned that claim, although there is broad agreement that the North is moving ahead quickly with both its nuclear and ballistic missile programmes.
The type of South Korean missile tested Wednesday is capable of carrying a one-tonne payload up to 500 kilometres (310 miles).
A similar missile was previously tested in April 2014.
The United States stations 28,500 troops in South Korea and guarantees a nuclear "umbrella" in case of any atomic attack.
In return, Seoul accepts limits on its missile capabilities and had previously operated under a range and payload ceiling of 300 kilometres and 500 kilograms (1,100 pounds).
Given the ambitions of North Korea's own missile programme, the South had long argued for the limits to be extended.
While the maximum payload for that range remains 500 kilograms, the two parameters are inversely linked, so that for shorter ranges corresponding payload increases are allowed.
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