The match official dished out an astonishing 28 penalties - including a world-record 19 attempts at the posts - as he pulled up a number of infringements at the set-piece. In the end, it was the perceived indiscipline of the hosts that cost them a 28-18 defeat and ultimately their chance to challenge leaders England for the RBS 6 Nations title.
Johnson did admit that he was baffled by some of the decisions that went against his team, but the Australian refused to point the finger at the referee as he insisted the reason for the defeat was the fact Scotland failed to make the most of the little ball they had. Asked about Joubert's numerous interruptions, he said: "It didn't make for a great spectacle."
Johnson added: "But I'm not here to discuss referees. He's got a job to do and he seems a decent bloke. I don't want to be the guy who talks about referees when he loses. The frustrating thing for us is that we had our first line-out in the second half. We think we are a competitive scrum, but we got to play off nothing.
"We let ourselves down but Wales took the most of their opportunities. There is nothing much between those two sides. That bodes well for us because they are world class.
"But we need to look at ourselves. We can try to find excuses and different reasons why that game didn't go our way. But I'd rather work on what we can do. We can't play Test match rugby like that and we don't want to.
"You score tries off set-piece, but we are not getting set-piece. It's that inability to play off a platform that is stopping us. We had one scrum just before half-time five metres off the line. It was perfect platform to play off. But what happened? We ended up 60 metres back down the track.
"We're always under the cosh. But what we are showing is great resolve. We are defending like mad men. But it would just be nice to have it where we can play a bit."
Wales will now face England next week with the championship on the line. Caretaker boss Rob Howley paid tribute to man-of-the-match Sam Warburton after the flanker returned to the team after two games out to contribute to his side's win.
Howley said: "I was pleased with the victory. Murrayfield is not the easiest place to come. Many good Wales teams have come down the years and lost. I thought our pack was outstanding. In terms of their ball carrying and defensive qualities, were looked fairly strong. That gave us the platform and we need that. In attack and defence, Sam Warburton was outstanding.
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