Beijing bristled when the deal, to be signed off at annual security talks, was announced as part of the US "pivot" to Asia in 2011.
But Bishop, who is hosting US Secretary of State John Kerry and Defence Secretary Chuck Hagel in Sydney, said the rotation of Marines into the northern city of Darwin was the "natural evolution" of their alliance.
"It's aimed at supporting the long-term peace, stability and prosperity of our region, the Indian Ocean-Asia Pacific," she said ahead of the Australia-US Ministerial Consultations (AUSMIN).
"That's not what it is directed to do at all. It's about working closely with the United States to ensure that we can work on regional peace and security," she told the Australian Broadcasting Corporation.
"The United States is rebalancing to the Asia-Pacific so it's ways we can work together to support economic development as well as security and peace."
Bishop downplayed the prospect of an increased US military presence beyond the 2,500 Marines and Air Force personnel, though analysts have said the allies will likely look to boost the US assets in future.
"It's an opportunity to discuss our shared perspectives and approaches on major foreign policy strategic development."
Hagel said yesterday the Marine rotation emphasised Washington's "rebalance" towards the region, saying the United States was a Pacific power which was "not going anywhere".
"It's pretty clear that the US is committed to this part of the world but also this does not mean a retreat from any other part of the world. We have interests all over the world," he said.
Speaking at the start of the talks at Sydney's harbourside Admiralty House, Kerry said the Australia-US relationship was "essential to the stability of the Asia-Pacific region".
