Shane Duffy rose to bundle the ball in but referee David Borbalan ruled out the goal for a foul on Konrad Laimer.
"There's nothing wrong with it at all - he's called a foul on Shane Duffy and I can't see it," said O'Neill.
"We were very sloppy in the first half but went roaring into it in the second half and got the goal."
Martin Hinteregger's strike gave Austria a first-half lead but an improved Republic levelled with five minutes left thanks to a Jon Walters volley.
The Republic stay second and level on points with leaders Serbia, who drew 1-1 with Wales.
O'Neill added: "We were fantastic in the second half in terms of drive and energy and we were hard done by. I thought Duffy's disallowed goal was a goal.
"Jon Walters epitomised the strength and character this squad possesses. Second half, we were really terrific.
"I have to say we were backed by a ferocious crowd. They were absolutely magnificent and really helped us."
Stoke forward Walters was happy that his goal maintained the Republic's unbeaten record in the qualifying campaign.
"The first half, we were slow," Walters told RTE Sport. "It was the opposite of what we said we'd do and the opposite of what we did against Uruguay.
"We're still unbeaten, we're still in it. We said there would be ups and downs in the qualifiers but we're still in it."
The Republic of Ireland were harshly denied a late winner in Sunday's 1-1 World Cup qualifying draw with Austria, manager Martin O'Neill said.