The three field umpires - Brett Rosebury, Matt Stevic and Shaun Ryan - did not pay Johnson any free kicks during the match despite Baker's close checking and eventual nine-week suspension for it.
Umpire boss Jeff Gieschen said the trio of umpires still rated in the League's top six and did a "terrific" job despite failing to see any of the incidents involving the two players.
"For people to suggest they just stood by and watched and ignored what happened is just not accurate at all," he told afl.com.au on Wednesday.
"The basic philosophy is, for an umpire to intervene and do something, he's got to see it.
"In the cases of Baker and Johnson on the weekend, they were very cunning and did it at times the umpire simply couldn't see.
"We would have loved one of the umpires to see the high contact and pay a free kick, perhaps make a report, because we know that type of intervention is the best type of deterrence.
"These incidents were in isolation. It wasn't as though Baker and Johnson stood there for 30 seconds or even 15 seconds remonstrating with each other. If they had done it continuously, the umpires were going to become aware of that.
"You take out not being able to see these incidents, and one or two mistake free kicks in the game, and by and large they did a fantastic job."
Gieschen watched the match from the umpires' observers box and was subject to constant audio of the umpires reminding the players to stop engaging.
"Throughout the game, we heard numerous occasions, in fact non-stop, basically, the umpires going to Baker and Johnson and telling them to settle down," he said.
"They were continually trying to manage that situation but while the umpires are there, Baker's not going to punch and Johnson's not going to whack him.
"They're going to settle down. As soon as they settled down, the umpire turned his focus back to the ball and as soon as he turns his back, that's when things happen again.
"It was very difficult for the umpires to manage but they certainly tried their hardest."
Gieschen also defended the involvement of emergency umpire Stefan Grun, and said he had successfully made the field umpires aware of scuffles between the players.
"He can't pay a free kick when he's sitting on the bench. The only time he can pay a free kick is if he's out on the ground near the players and he sees something clearly as well," he said.
"He was working overtime; not just helping the umpires with the Baker-Johnson scenario, but he was also assisting them with holding at stoppages and who were the taggers, etc.
"It wasn't as though he was sitting there doing nothing."
Gieschen said the League would consider if the playing field was adequately resourced with umpires and if the role of the emergency umpire needed to increase across the rest of the season.
