The biggest of the outbreaks, centred on a Brisbane veterinary clinic, claimed the life of veterinarian Ben Cunneen.
The other was in Proserpine, in northern Queensland. Yesterday, the state's Department of Primary Industries lifted the quarantine on that property after final laboratory testing confirmed the rare Hendra virus is no longer a risk.
The North Queensland property was quarantined on July 14 after a local vet contacted the department over concerns a local horse was exhibiting Hendra virus symptoms.
Subsequent testing confirmed three out of the five horses that lived on the property had contracted the rare virus, which is carried by native fruit bats.
Chief Veterinary Officer Dr Ron Glanville said in considering when to lift the quarantine, Biosecurity Queensland's top priority was to ensure there was no evidence of the virus remaining, and that both humans and other horses were protected against any possible spread.
"I would like to thank the property owners for their ongoing assistance during this time, as well as the local vet who moved quickly to report the case to us," he said.
"I encourage anyone with concerns about Hendra virus to contact their local veterinarian or Biosecurity Queensland immediately."
All three of the infected horses died from the virus, including a horse euthanised by Biosecurity Queensland.
Scientists from the department and the Australian Animal Health Laboratory carried out a post mortem on the horse in a bid to learn more about the rare disease.