Minesweeper HMAS Gascoyne found the ordnance, which was jettisoned by two US AV-8B Harrier jets during bilateral war games with Australian forces in July.
The jets had intended to drop the two BDU 45s and two GBU 12s on an island in the Shoalwater Bay military training area, but had to ditch them in waters within the Great Barrier Reef Marine Park after civilian boats strayed into the drop zone.
They were found at a depth of 60-70 metres using a remote-controlled submersible equipped with sonar.
"HMAS Gascoyne has complied with all environmental regulations throughout the search and the bombs were positively identified using one of the mine-hunter's remote operating vehicles," said Lieutenant Ash Power, joint operations chief.
"At no stage did the jettisoned ordnance pose a threat to the safety of people or the Great Barrier Reef."
Navy said retrieval of the bombs in conjunction with the USS Germantown would depend on weather conditions and environmental factors.
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