Griffith University, University of New South Wales and University of Technology Sydney will work with Duke University, the University of Oregon and the Massachusetts Institute of Technology on integrated quantum sensing and control for high fidelity qubit operations.
Sydney University and the University of New South Wales will partner with the University of Tennessee, Ohio State University and Virginia Polytechnic Institute on a project in material sciences.
Minister for Defence Industry Christopher Pyne congratulated the universities, saying the success was thanks to the Next Generation Technologies Fund, and was the first time Defence had funded Australian universities to work with their US counterparts.
While Australian universities could bid for MURI projects in the past, they were not eligible for grants from the US Department of Defense.
"The government is investing $25 million in the Australian version of the MURI program, called AUSMURI, to facilitate joint research with the American universities," Minister Pyne said.
"As these universities were chosen from a pool of over 400 proposals, this is a great outcome, one which shows that Australian researchers are world class."
The Australian universities will each receive a grant of up to $1 million per year for three years to support their research in Australia.
Defence and the US DoD have also selected the next topic eligible for funding under AUSMURI 2019 - active perception and knowledge exploitation in navigation and spatial awareness.
"Research in this area will enhance the manoeuvrability of people and autonomous platforms in environments where traditional navigation systems are ineffective," the minister said.
"The AUSMURI program enables Defence to access the best research expertise from Australia and the US to develop game-changing military capabilities."