The MV-22B Osprey came down on a remote island north of Darwin on Sunday.
Captain Eleanor LeBeau, 29, Corporal Spencer Collart, 21, and Major Tobin Lewis, 37, were killed and the 20 other people on board - all US marines - were injured.
The cause of the crash remains under investigation.
In a statement on Tuesday, the commanding officer of the Marine Rotational Force Darwin said the force was "deeply saddened" by the loss of such "respected and beloved" marines.
Capt LeBeau - originally from Illinois - was piloting the Osprey and had served in the marines for five years, while Cpl Collart - from Virginia - enlisted in 2020.
Maj Lewis - from Colorado - was a highly decorated leader with over 15-years' experience in the marines, and was the executive officer on board the aircraft.
"Our thoughts and prayers remain with the families and with all involved," Col Brendan Sullivan said, adding that his team remained focused on ongoing recovery and investigative efforts.
The aircraft had been participating in Predators Run, a training exercise involving 2,500 troops from the US, Australia, the Philippines, East Timor and Indonesia, when it crashed on Melville Island.
Soon after, air traffic control were heard discussing a "significant fire" at the site, according to audio obtained by local media.
All 20 marines who survived the crash were taken to hospital. One remains in a critical condition, and another two are in hospital but stable.
The incident is the second fatal air crash during joint exercises in northern Australia in less than a month.
On 29 July four Australian soldiers died after their 45 MRH-90 Taipan crashed off the coast of Queensland while participating in Exercise Talisman Sabre, the largest bilateral military training exercise between Australia and the US.
The latest incident is one of several recent crashes involving an Osprey - a helicopter and turbo-prop plane hybrid.
Four marines were killed in a crash in Norway last year, and three others died in 2017 when their aircraft clipped the back of a transport ship off northern Australia.