Greig Laidlaw will wear the armband in the second viagogo Autumn Test at Murrayfield and Scarlets flanker John Barclay comes in for Brown.
Johnson made six changes in all with at least one enforced as Saracens back Duncan Taylor makes his first start in place of injured Edinburgh centre Matt Scott.
Props Alasdair Dickinson and Moray Low come in along with locks Jim Hamilton and Richie Gray, whose younger brother Jonny is on the bench.
Johnson has made it clear before the series that he would utilise his squad in a bid to deepen Scotland's player pool ahead of the 2015 World Cup, and that long-term strategy meant Brown was always going to sit out the middle Test.
"That was part of the plan, he was never going to play this game," Johnson told Press Association Sport.
"We predicted the Japanese game was going to be fast and furious, the back row would have done a lot of mileage. We knew that and we have a six-day turnaround at the back end.
"So it's us being half-smart, and it gives us the opportunity to see other combinations. Kelly will be seen in the Aussie game. That's just the way we have to do things. We have got to be smart here.
"We are sticking to our plan. It gives us the opportunity to see how guys can stand up against the big boys."
Taylor, 24, will make his home debut after coming off the bench during each of Scotland's three summer games after Scott suffered a hand fracture that will keep him out for about six weeks.
Johnson said: "I see injuries as opportunities for people. We have got a lot of backs out but it's a great opportunity for others.
"It gives Duncan a run and we are keen to have a look at him.
"His form with Saracens has been terrific. He has got an industrious work-rate, he has good core skills. He's a big man. A lot of boxes ticked there."
Also missing out is Euan Murray, who drops out because of his religious beliefs while Ryan Grant, who went off in the first half against Japan with a head knock, drops to the bench.
Alastair Kellock, who also suffered concussion, and man of the match Tim Swinson, who picked up a shoulder injury but was available for selection, miss out.
On lock Swinson, Johnson said: "He was never really going to play this game but he made us review it. The fact is we didn't want to be sitting around and discussing it, we stuck to the plan. We have a pretty good combination going out there on Sunday."
Meanwhile, Johnson remained largely neutral about Scotland's 42-17 on reflection after being torn between positivity and negativity on Saturday night after his side hit back immediately following both Japan tries.
"I was 51 per cent positive," he said. "The scoredboard won me. The 49 per cent, we have still got to be honest with the fact we need to improve on some things.
"I only moved one per cent. I felt pretty good. I slept all right."
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