The New Zealand mentor was most upset that Joe Tomane's 50th-minute try, for a 27-16 lead, was allowed to stand after an Israel Folau pass floated marginally forward.
The English whistle-blower had called for the television match official (TMO) to show him a replay on the big screen and adjudged that Folau passed the ball backwards out of his hands.
"We thought it was forward," Gatland said.
"The referee made the decision himself, without the TMO.
"I doubt he would have made that decision himself if it was the All Blacks playing," he added in a shot at the prolonged Kiwi outcry following Barnes missing a French forward pass in New Zealand's famous 2007 World Cup capitulation.
Gatland also argued that Wales could have been handed a penalty try with five minutes left when Quade Cooper tackled Scott Williams as, or just before, he received a Dan Lydiate pass on hot attack.
Barnes sin-binned Cooper in what was a contentious decision, one which had the Australian camp up in arms.
Neither side were happy with the flow of breakdown penalties in what was otherwise a cracking test match.
Welsh five-eighth Dan Bigger was sin-binned late in the first half for a blatant ruck infringement after pulling Folau down on the line.
While he was off the field, the Wallabies scored 10 points.
With the Wallabies' back-row superior, Gatland claimed Australia were lucky not to have had someone yellow-carded as well.
"They were smart in the way they played," he said.
"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."
Although Wales have lost 23 of their past 24 Tests to the three Southern Hemisphere heavyweights, he felt they were "knocking on the door".
"We said to the boys to back yourselves and back your fitness and I think it was an Australian team that was falling into a hole at the end."
Meanwhile, a Barbarians side packed with Springboks and All Blacks had too much power and pace for an understrength Fiji and won their match celebrating Fiji's centenary 43-19 at Twickenham on Sunday.
Charles Piutau and Tom Taylor scored for the Barbarians as the side crossed over seven times.
Fiji were forced to release several senior players to their French and British clubs because the match was outside the test window.
- AAP
