Lance Corporal Richard Parker and Private Peter Gillson were killed during battle in the Dong Nai province east of Saigon in 1965, but their bodies were never recovered.
The group of veterans, known as Operation Aussies Home, have been searching in Vietnam for the two soldiers and another four still missing in other parts of the country.
Group leader Retired Infantry Lieutenant Colonel Jim Bourke and Veterans Affairs Minister Bruce Billson are both optimistic the remains will be identified as the missing pair.
Lt Col Bourke said the group had researched their likely resting place then used ground-penetrating radar to eliminate much of the half-acre cassava field they were examining.
On Monday the group discovered the sole of a boot and began excavating the surrounding area.
"(On Wednesday) we had a major breakthrough," Mr Bourke told ABC Radio.
"The guys recovered a map that was the same map as we used on that operation in 1965.
"It was quite a moving scene, actually.
"The men were working in extreme temperatures, and as they were excavating they were talking to their friends, and telling them they were going home."
Lt Col Bourke said he had called the men's families to break the news.
"I didn't want to do it until I was 99.5 per cent certain that we had the remains of the two men, and I've got that degree of certainty now, based on the recovery of the map," he said.
"Obviously identification of the remains will be subject to a formal forensic process. But as I say I'm 99 per cent certain that we're on the money."
Mr Billson said if the remains did prove to be Australian they would be treated with dignity.
"We've got some optimism but we need to be careful that there's firm (proof of their identity)," he told Southern Cross Broadcasting.
"I've got some optimism, if they are who we think they may be, we'll arrange for their repatriation back to Australia and proper burial in consultation with their families."
Forensic specialists were preparing to leave for Vietnam within days to help in the identification process, Mr Billson said.
The excavation also has uncovered bone fragments, teeth and a button used on Australian Army clothing of the 1960s.
AAP