The injury - sustained in the bruising encounter against Georgia in Cardiff - isn't serious, and All Black coach Steve Hansen was at pains to stress his No7 could have played if necessary.
"If we were playing a final he'd be fine, but we're just not prepared to take any risks with anyone who's not 100 per cent," Hansen said.
"He can have a breather and it gives Liam [Messam] an opportunity to come off the bench and get some footy and Sam [Cane] can get a start.
"He got a bang on his thigh so it's just a bit sore when he stretches out at top-end pace. It's just not worth risking it."
Asked about the reaction at home from people concerned at McCaw's wellbeing after his injury problems at the last World Cup, Hansen said: "We're okay with it and people who are anxious about it don't need to be anxious."
Cane will wear the No 7 jersey, and No 8 Kieran Read will captain the team. Messam, a late withdrawal from the Namibia match due to a calf strain, gets his first opportunity for game time.
Prop Charlie Faumuina was unavailable for selection due to a tight hamstring for the test at St James' Park, but wing Waisake Naholo has recovered from his bruised leg and will start on the left wing, replacing Julian Savea, with Nehe Milner-Skudder on the right wing.
Midfielder Ma'a Nonu, starting in the No12 jersey, will celebrate his 100th test milestone.
"On behalf of the All Blacks, I would like to congratulate Ma'a on this special milestone," Hansen said.
"He has been an incredibly valued member of our group for a very long time. He has been fully committed to enhancing the All Blacks jersey and the values that go with it."
Luke Romano and Sam Whitelock are the starting locks, with Brodie Retallick on the bench, a more traditional cover model than the All Blacks' recent trend of having two loose forwards there.
Props Tony Woodcock and Owen Franks return to their starting roles after giving way to Wyatt Cockett and Faumuina at the Millennium Stadium.
The All Blacks, with three wins from three in pool play, are comfortable with where they are, but are keen for a more complete, mistake-free performance, than their one against Georgia.
"We've had a very heavy workload in the last two weeks on the training pitch and a couple of very physical games, which has been great," Hansen said.
"But this week we've been looking to freshen the group up and really concentrate on the key parts of our game that we expect will deliver a quality, 80-minute performance on Friday night. We're getting to the exciting part of the competition - one game out from knockout footy."
The All Blacks' quarter-final opponents will be the loser of the France v Ireland pool game at the Millennium Stadium on Monday morning NZT.
All Black team to play Tonga in Newcastle on Saturday morning (8am NZT)
Tony Woodcock, Dane Coles, Owen Franks, Sam Whitelock, Luke Romano, Jerome Kaino, Sam Cane, Kieran Read (c), Aaron Smith, Dan Carter, Waisake Naholo, Ma'a Nonu, Conrad Smith, Nehe Milner-Skudder, Ben Smith. Reserves: Keven Mealamu, Wyatt Crockett, Ben Franks, Brodie Retallick, Liam Messam, Tawera Kerr-Barlow, Beauden Barrett, Sonny Bill Williams.
- Patrick McKendry in Darlington
