The drills come after Pyongyang tested a series of short-range projectiles in recent days, calling one of them a "solemn warning" to Seoul against pursuing the mainly computer-simulated drills with Washington.
South Korean defence minister Jeong Kyeong-doo told parliament that the joint exercise began Monday, adding that Seoul was "clearly maintaining its readiness posture against any military action by North Korea".
Details about the training have not been disclosed, but a ministry official in Seoul said this year's exercise will include verifying South Korea's abilities to take operational control in wartime.
Under the US-South Korea security treaty, an American general will take command of their combined forces in the event of armed conflict, but Seoul has long sought to reverse the position.
Analysts say the military activities by both sides could delay talks on the North's weapons programmes -- which have seen it subjected to multiple sets of UN Security Council sanctions -- until later this year.
After a year of mutual threats and mounting tensions, US President Donald Trump and the North's leader Kim Jong Un held a historic meeting in Singapore last year, when Kim signed a vague pledge to work towards "denuclearisation of the Korean peninsula".
A second summit in Hanoi in February broke up amid disagreement on sanctions relief and what the North might be willing to give up in return.
Trump and Kim agreed to resume nuclear talks during their impromptu June meeting in the Demilitarized Zone that divides the peninsula, but that working-level dialogue has yet to begin.
The nuclear-armed North -- which attacked its neighbour in 1950, triggering the Korean War -- has always been infuriated by military exercises between the US and the South, decrying them as rehearsals for invasion.
After the Singapore summit, Trump made a shock announcement halting joint drills, adopting Pyongyang's own description of them as "provocative" at an extraordinary, freewheeling press conference.
War games known as Ulchi Freedom Guardian (UFG) and scheduled for August last year were subsequently suspended.
And the allies' biggest annual drills, Foal Eagle and Key Resolve, which took place every spring and involved tens of thousands of troops, were replaced with a shorter "Dong Maeng" or "Alliance" exercise in March.
- 'Changing stance' -
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The August drills were scaled down earlier this year, Yonhap news agency reported, and have not been named, with an official from Seoul's Joint Chiefs of Staff (JCS) telling AFP that they "cannot comment any further" on their designation.
South Korean media have dubbed the command post exercise "19-2 Dong Maeng", indicating the second Dong Maeng exercise of 2019.
Pyongyang warned last week that further nuclear talks could be derailed if Seoul and Washington push ahead with the manoeuvres.
And on Friday, North Korea carried out its third weapons test in the space of eight days, firing what it called a new "large calibre multiple launch guided rocket system".
Seoul's presidential office said it was highly likely to be "a new type of short-range ballistic missile".
Ahn Chan-il, a North Korean defector and researcher in Seoul, told AFP: "Drills might not have taken place today if there had been some concrete progress with the nuclear negotiations between Pyongyang and Washington, considering UFG was suspended last year."
The North's recent launches also affected the allies' decision, he added. "This also signals Seoul's changing stance on Pyongyang."
Trump has brushed off the North's tests, saying Kim will not want to "disappoint" him because he has "far too much to lose".
"He will do the right thing because he is far too smart not to, and he does not want to disappoint his friend, President Trump!" he said.
There are 28,500 US troops stationed in South Korea to protect it against its neighbour, many of them based south of Seoul at Camp Humphreys in Pyeongtaek -- Washington's biggest overseas military facility.