And with captain Chris Cusiter was ruled out of the first Test with injury, head coach Andy Robinson has sided with the Gloucester back over co-captain Blair, whose season was curtailed by injury and loss of form.
"Rory has performed well for Gloucester at the end of the season," said Robinson. "You have to view this on merit.
"I think we have three outstanding scrum-halves and I believe it is right to pick Rory.
"Mike is a quality performer and he will still have an influence on the game at the weekend."
Having led Glasgow Warriors into the inaugural Mangers League play-offs this season, lock Kellock will take the armband while teammate Moray Low will fill in at tighthead for Euan Murray.
Scotland: Southwell (Stade Francais), Evans (Glasgow Warriors), De Luca (Edinburgh), Morrison (Glasgow Warriors), Lamont (Scarlets), Parks (Glasgow Warriors), R Lawson (Gloucester), Jacobsen (Edinburgh), Ford (Edinburgh), Low (Glasgow Warriors), Hamilton (Edinburgh), Kellock (Glasgow Warriors), Brown (Glasgow Warriors), Beattie (Glasgow Warriors), Barclay (Glasgow Warriors)
Replacements: S Lawson (Gloucester), Cross (Edinburgh), MacLeod (Edinburgh), Strokosch (Gloucester), Blair (Edinburgh), Godman (Edinburgh), Thompson (Edinburgh)