Police said the 26-year-old man was defending himself with a samurai sword-style weapon when he was shot in the lower body, likely by a shotgun.
Emergency services were called to a Nundah property shortly after midnight following multiple reports of shots fired, police said.
Up to five men allegedly broke into the Florence Street residence in Brisbane's north.
"The occupants have only been at that address approximately in the last month," Detective Inspector John Mison said on Thursday.
The man was later shot outside the unit complex, police said.
It's believed the weapon used was mostly likely a shotgun, due to the "pellet type of injuries", Det Mison said.
"I'm aware that the male person armed himself, which led to some of the offenders fleeing the residents," he said.Â
"That may have been a ... samurai sword and that would potentially be why the intruders, I suppose, opened fire in retaliation."
The 24-year-old woman sustained minor "shrapnel-type injuries" in the incident.
The man and woman were transported to hospital with non-life-threatening injuries.
The group of "three to five" intruders left before police arrived, Det Mison said.
Police are conducting door knocks and analysing CCTV around the area, he said.
Anyone with information or CCTV and dashcam footage should contact police.
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