But Gatland believes Israel Folau's pass to Tomane was forward.
"The referee made the decision himself, without the TMO. I doubt he would have made that decision himself if it was the [New Zealand] All Blacks playing," said Gatland.
"He made the call himself. I haven't spoken to him about it. It is not going to change the result."
Wales fought back to within four points of Australia but could not prevent a ninth successive defeat by the Wallabies.
"We are knocking at the door at the moment, and at some stage we are going to knock it over," insisted Gatland, who guided a Welsh-dominated Lions side to a 2-1 series victory over Australia in the summer.
Late in the game referee Barnes sin-binned Australia fly-half Quade Cooper after he tackled Scott Williams before the Wales centre received the ball.
Wing George North picked up the loose possession and had a clear run to the line, and Gatland said Barnes could "arguably" have awarded a penalty try.
Instead Wales opted to kick for touch and have an attacking line-out, but the tactic failed and Australia held out.
Gatland reflects on 'epic' match
"It was a great game of rugby if you were a neutral or an Australian. It was a real Test match out there," Gatland said.
"We are knocking on the door. The thing is with the southern hemisphere now, which is different to the past, is that they are coming here fully loaded and not making changes.
"We dug deep, and we showed courage to come back. Our fitness looked good in the second half, and we put ourselves in a position where we had a chance to win it."
Gatland praised his players for "digging deep" but admitted some of their decision making would come under question when the game is reviewed.
"It was frustrating that of the 18 penalties we got, I think 14 were at the breakdown, which stopped some of the momentum we were trying to create," he said.
"We will review a few things in the game, whether we would have made different decisions that might have affected the outcome, but I just thought the last period of the game we looked pretty good.
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