Paul and Mandi McDonald, 45, were at their Moyhu farm, about 260km from Melbourne, on Wednesday morning when the tragedy occurred.
She suffered life-threatening injuries, and was immediately flown to hospital.
Local resident Patrice Larkin said she knew the couple well.
The deer badly injured his wife when she came to her husband's aid, police said.
Police killed the deer at the scene, Victoria Police said.
According to police the Waipiti deer - a cross between a red deer and an elk - had been a pet of the family for about 2 years.
Autumn is mating, or rutting, season for many species of deer, and is a particularly risky time to be around the wild animals.
'The deer was shot a number of times for the safety of the male and the female, ' Acting Senior Sergeant Paul Purcell said.
'They are a wild animal and a wild animal that loses its fear of humans is a really risky thing, ' he told Herald Sun.
A warning has been issued after a man was killed by a deer in Victoria.
"It's tragic but not unheard of", Mr Howlett said.
He added that Australia's deer farming industry, where valuable velvet is extracted from antlers, has "declined greatly over the last 20 to 30 years".
But feral populations have since expanded across the country with increasing calls for greater controls in many areas where they are considered a pest.