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And in another, unforced, change, Neil Wagner has replaced veteran Chris Martin in a three-pronged fast-medium attack in which two bowl with the left arm.
Franklin strained a hamstring bowling in the nets on Wednesday and is expected to be sidelined for a few days.
However, he is expected to be fit for the three-game ODI series to follow the second and final test.
Munro, born in Durban but who moved to New Zealand with his family at age 15, makes his debut batting at No 7 and offering some back up medium pace.
Growing up Munro admitted playing for New Zealand wasn't part of his cricketing dreams. He relished graduating into the South African team.
"But after going through the (New Zealand) age groups and playing for New Zealand at under 19 level I got a taste for it," he said.
"Playing for New Zealand is a great honour."
His ambition out of the match is simple: "A win, that's all. It would be massive, and secondly would be contributing to that win."
He reckons he's seeing the ball well, and he has been plundering domestic runs for Auckland but "obviously it's a huge step and time will tell whether I'm ready for test cricket".
Munro is expecting some verbal advice from the South African players and plenty of short pitched bowling. But he's a solid horizontal shot maker which could stand him in good stead.
New Zealand captain Brendon McCullum likes the 25-year-old's attitude.
"He plays the game with a free spirit and has earned the right to be in the squad. We think at No 7 in the line-up he could be quite counter-attacking for us."
Wagner, born in Pretoria, has already played two tests in the West Indies last year, picking up four expensive wickets.
He owes his selection to two factors: he's been impressive in the nets in the last few days and his ability to reverse swing the old ball on a St George's Park pitch which is expected to rough up the ball.
"Chris got the first opportunity and did an okay job," McCullum said.
"Whilst he got three wickets later in the test and bowled reasonably well, we felt the more aggressive option of Neil, especially with the potentially drying pitch would serve us better to try and even up the series."
As McCullum put it: "All roads pointed to Neil in this test."
"He's a lovely guy, and plays the game hard on the field. We expect him to play extremely hard especially being from South Africa himself. We're confident he'll turn out and put in a really good performance."
There is one other conundrum for McCullum and the coaching staff to consider. Left arm spinner Bruce Martin is in the 12, as is offspinner Jeetan Patel.
If their reading of the pitch before the toss is that it might break up relatively early in the match, they could play both spinners. But McCullum made it clear Patel is first choice.
The hope is that the rough created by left armers Trent Boult and Wagner will give Patel some assistance.
Patel's lame batting down the order in the first test at Cape Town wasn't a factor, McCullum said.
"He didn't exactly cover himself in glory in the last innings but he wasn't the only one.
"Ultimately Jeetan is a bowler and if we can take some of the sting out of their attack then our lower order won't be exposed to quite the same extreme circumstances as they were in the last test."
New Zealand must win the test to square the series with the world No 1 test team.
The hosts have made only one change, Vernon Philander's hamstring strain ruling him out, his place going to Rory Kleinveldt.
It's a small mercy for New Zealand's batsmen, but they hope the anticipated lower bounce, and slower pace of the St George's Park pitch will help reduce the effectiveness in terms of hostility of Dale Steyn, Morne Morkel and Kleinveldt.
South Africa have lost their last three tests in Port Elizabeth, so they feel a sense of wanting to get back to winning ways.
They are expecting much more from New Zealand in conditions they believe will be most akin to those back home for the tourists.
Wagner will stay on for the ODI series against South Africa as a replacement for Central Districts bowler Adam Milne.
He has had a recurrence of a lower leg injury and is unable to bowl without pain. Further assessment is required to determine the severity of the injury.
Already Wellington veteran Grant Elliott is joining the squad for the 50-over series as a replacement for injured Northern Districts' allrounder Corey Anderson.