London Irish full back Delon Armitage replaces 2005 Lion Mark Cueto on the wing having started against Argentina and Georgia while the Sale star was struggling with a back injury.
Courtney Lawes returns from a two-match suspension for kneeing Argentine hooker Mario Ledesma and is immediately recalled to the first-choice XV where he will partner Leicester's Louis Deacon in the second row.
The third and final change sees Matt Stevens, another 2005 Lion, take over from Alex Corbisiero at loose-head prop.
But while the inclusion of Stevens and Lawes was expected, the demotion of Cueto appears a more contentious call.
The 31-year-old had featured in all 10 games in the past two RBS 6 Nations' campaigns, as well the two summer Tests in Australia and the four November internationals at Twickenham in 2010.
Cueto then played in all three World Cup warm-up matches before a lower back injury forced him off the field during the win over Ireland in late August. That injury kept him out of England's opening two tournament victories but he was fit enough to return to action against the Romanians.
And the 54-cap veteran did more than just get through his first appearance of the competition as he claimed a hat-trick of tries. It wasn't enough to see him keep his place, however, with Johnson admitting Cueto is not quite back to his best.
"We've said all the way through if Delon's playing well and with form he's a Test player," said Johnson, after Cueto dropped out of the matchday 22 altogether.
"Mark's injury was a factor. He's probably a game short of being back to where he should be."
James Haskell retains his position at No8 despite Nick Easter's availability after injury, with Jonny Wilkinson starting at outside-half ahead of Toby Flood.
England will be without two of their coaching staff on Saturday, though, after fitness specialist Paul Stridgeon and kicking guru Dave Alred were suspended for one game by the Rugby Football Union.
The duo were found to have helped Wilkinson illegally switch balls when lining up two conversions against Romania, with the International Rugby Board instigating an investigation.
England have responded by removing the pair from duty this weekend and the IRB have responded by stating that the matter is now closed.
"It's unfortunate that we have had to take this action but ultimately there was a breach of the laws of the game," added Johnson.
"But it's happened, some action has been taken and we have to move on."
England ( vs Scotland Auckland, Saturday, 8.30am BST)
Ben Foden; Chris Ashton, Manu Tuilagi, Mike Tindall, Delon Armitage, Jonny Wilkinson, Ben Youngs; Matt Stevens, Steve Thompson, Dan Cole, Louis Deacon, Courtney Lawes, Tom Croft, Lewis Moody (captain), James Haskell
Replacements: Dylan Hartley, Alex Corbisiero, Tom Palmer, Nick Easter, Richard Wigglesworth, Toby Flood, Matt Banahan
NB Bold denotes Lion