The Perpignan blindside has been replaced in the starting XV by John Barclay, who is promoted from the bench to start at openside flanker.
Captain Kelly Brown will revert to blindside, with David Denton remaining at number eight and uncapped Edinburgh back-row Stuart McInally named among the replacements.
The loss of Strokosch, who performed well against New Zealand, particularly in defence, is a blow.
It is the third change from the side which began the 51-22 loss to New Zealand last weekend and second in the back row after Ross Rennie dislocated a shoulder and was replaced by Denton.
Scotland head coach Andy Robinson said: "We wish 'Stroker' a speedy recovery.
"John is an experienced campaigner, while Stuart was with us on the summer tour and is raring to go."
Scotland team doctor James Robson said: "Alasdair suffered a minor calf strain in training this week and while we were hopeful it would settle in time we believe his recovery has not been sufficient to warrant risking a partially-fit player."
Glasgow Warrior Barclay, who was man of the match when Scotland beat South Africa in November 2010, will win his 40th cap.
McInally has captained Scotland at every age grade and represented Scotland sevens and Scotland A.
The other change to the Scotland team sees tighthead prop Euan Murray, who was unavailable against the All Blacks due to his refusal to play on Sundays for religious reasons, return.
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The entire All Blacks apparel line has been updated for 2013/14. Check out the New Zealand All Blacks polo.
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