The two missiles, with a range of 305 miles, were fired from the western city of Nampo into the sea east of the Korean peninsula, the South Korean military said.
The drills, involving tens of thousands of troops, always anger Pyongyang.
It traditionally shows its displeasure with missile tests and louder rhetoric.
Seoul and Washington describe the military exercises as defensive in nature. North Korea calls them a rehearsal for invasion.
Key Resolve, a largely computer-simulated exercise, lasts 12 days and Foal Eagle, which has ground, air and sea components, lasts eight weeks.
In a statement, South Korea’s Joint Chiefs of Staff said the missiles, fired on March 2, were probably Scud Cs or Scud Ds.
The military remained “vigilant against any additional launches”, it said.
South Korea’s Defense Minister Kim Min-seok vowed a stern response to any provocation.
“If North Korea takes provocative actions, our military will react firmly and strongly so North Korea will regret it in its bones,” he was quoted as saying by Reuters.
Earlier in the day the North Korean military condemned the joint exercises as “undisguised encroachment” on national sovereignty.
Aggression should be dealt with by “merciless strikes”, it said in a statement carried by KCNA news agency.
In 2013 the joint exercises led to a prolonged surge in tensions, with North Korea threatening pre-emptive nuclear strikes and cutting a military hotline with the South.
Drills in 2014 passed off relatively quietly, however.
In January 2015, North Korea said it would offer a moratorium on nuclear testing if the joint exercises were cancelled. The US rejected this suggestion as an “implicit threat”.
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