The personnel change means a positional switch for Max Evans, who moves from the wing to outside centre.
But a high challenge by James on Max Evans gave sub Ruaridh Jackson the penalty to edge the home side in front.
Cardiff Blues-bound Dan Parks stays at stand-off after an impressive Six Nations comeback, while Max Evans and Sean Lamont will patrol the wings.
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The South African broke past Max Evans on the 22 and deftly touched down in the corner, under pressure from Morrison and replacement Hefin O'Hare.
Contepomi's conversion attempt was beyond the far post and the tourists looked for a quick reply but Max Evans was crowded out on the left flank.
Two minutes later, Glasgow finally put an attack together and from a sparkling counter-attack, Max Evans's chip eluded Vincent Clerc for Aramburu to grab the try.
France looked in trouble in the fifth minute when Sebastien Tillous-Borde fumbled a loose ball on his own tryline following a Max Evans kick and chase.
Chris Paterson and try-scorer Max Evans gave Scotland a much-needed cutting edge when they came on at Murrayfield, but they could not fashion a dramatic late comeback.
Fa'atau spotted the lack of cover to chip in behind the advancing line of red shirts and Max Evans fielded the bouncing ball deftly to go under the posts.
The move began with a Max Evans break in centre-field and finished with Parks side footing the ball to the left corner where Canadian Van der Merwe touched down.
The Stade Francais number eight is added to Saturday's 22, along with Rob Dewey, Max Evans, Mark Robertson, Nikki Walker, Simon Webster, Kelly Brown, Geoff Cross, Alastair Kellock and Alasdair Strokosch.
Glasgow had started brightly and O'Hare, who was a late replacement in the startling line-up for the injured Max Evans, went over the try line within the first couple of minutes following a clever dummy by Fergus Thomson.
Scotland's Max Evans, whose brother Thom suffered a career-ending broken neck against Wales last season, left the field on the stretcher and that seemed to encourage referee Dave Pearson to blow his whistle even though there was still time remaining on the clock.
The visitors looked more threatening in the opening 10 minutes than they had for the vast majority of last week's dismal defeat against Wales, with brothers Thom and Max Evans showing just why Scottish fans had been so disappointed to see them miss out at Murrayfield.
The Scarlets defensive line was again breached far too easily, with Thom Evans' brother Max handily involved from centre, and big number seven Barclay was in support to dive over.
Wing Thom Evans also helped himself to a brace, with brother Max and prop Moray Low joining in the fun.
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