The two bombers conducted a low-altitude flight over an air base located some 77km (48 miles) from the border between the two Koreas.
Pyongyang's latest nuclear test is believed to be its largest ever.
The US has warned the North of "serious consequences" in light of the test.
B-1B bombers are capable of carrying nuclear missiles and bombs that are able to destroy even underground bunkers.
North Korea has further been isolated from its neighbours since it announced that it had successfully carried out its fifth nuclear tests last week in defiance of UN resolutions.
South Korea has said it has a plan to annihilate the North Korean capital if it shows any signs of mounting a nuclear attack.
The North said the latest test had been of a "nuclear warhead that has been standardised to be able to be mounted on strategic ballistic rockets".
Estimates of the explosive yield of the latest blast have varied. South Korea's military said it was about 10 kilotonnes, enough to make it the North's "strongest nuclear test ever".
Previous nuclear tests North Korea claims it successfully conducted were in 2006, 2009, 2013 and in January. The yield of the bombs appears to have increased.
Other experts say initial indications suggest 20 kilotonnes or more. The bomb dropped by the US on Hiroshima in 1945 had a yield of about 15 kilotonnes.
The US has flown two supersonic B-1B Lancer strategic bombers over South Korea in a show of force, just days after North Korea carried out its fifth nuclear test.