The Dark Blues welcome the Auld Enemy to Murrayfield looking for major improvements after a dismal display against Ireland last Sunday.
The Scots opened up their RBS 6 Nations campaign with a 28-6 defeat, with Saracens flanker Brown a faint shadow of his usual combative self at the Aviva Stadium.
His number seven jersey goes to Glasgow's Chris Fusaro, with Johnson hoping the Scotstoun forward's ball handling skills will come in handy on a muddy Murrayfield pitch.
But that did not make the job of omitting Brown from his Calcutta Cup squad entirely any easier.
Johnson told Press Association Sport: "It was certainly one of the hardest decisions I've ever had to make as Scotland head coach, because there is a human side to this job.
"We are in the people's business and if you don't care for people you shouldn't be in it. I care for him and it was a tough decision.
"He's a guy I admire but it was the right decision."
Brown's omission is one of three changes to the starting XV following the loss to Ireland, with centre Matt Scott replacing the benched Duncan Taylor and Glasgow wing Tommy Seymour coming in for injured club-mate Sean Maitland, who has been ruled out the rest of the Championships with knee and ankle injuries.
Scrum-half Greig Laidlaw will lead the side out in Brown's absence while Johnson hopes Fusaro's skills will come in handy against England.
The Australian said: "Using my vernacular, he's a ground feeder. He's low to the ground and plays below a lot of people. The ball will be on the ground a bit and he reminds me of the type of player back home.
"His regional form has been good. I've asked him to change some things and to improve some things in his game and has done that, so he deserves his run out."
While the captain has been sacrificed, Johnson opted against dropping any of his front row, despite a flurry of criticism being aimed at hooker Ross Ford - who missed his target with five line-outs - and props Ryan Grant and Murray Low.
"We don't have many options, so let's be fair," said the head coach. "We can sit here and talk about possibilities in selection but let's talk about practicalities.
"If you want to tell people they are average, you will get an average performance. I don't coach like that.
"The players we have are the best this country has got. We have got to believe they will get better."
Scotland started brightly in Dublin but the longer they had the ball without crossing the gain line, they more rash they became.
But Johnson insists he has not been stung by the negative response to Sunday's display - because he does not read the papers.
"To be honest, I didn't have a scooby," he joked. "I wasn't aware there had been much criticism but I work on this theory: Ireland away is a pretty tough gig.
"Their provenances are all going pretty good. Scotland is on a different path. We could have gone down the same path as we have for the last few years and kept on getting the same results.
"I don't want to do that. I'll go another way. I might have a few more grey hairs but it wouldn't have been such a good ride.
"We need to make these changes and criticism is for somebody else to worry about."