Scotland team doctor James Robson said: "Nathan suffered a calf strain and aggravated an old ankle injury during the match at the weekend.
"Whilst the injury has settled considerably it is not at a level adequate for exposure to the rigours of test match rugby and therefore Nathan is withdrawn from selection."
Scotland coach Andy Robinson wished Hines a speedy recovery. He added: "I welcome Jim back into the squad following his own recovery from injury.
"We're going with Jim as he's like for like with Nathan and will help us to get a platform should we look to get our mauling game going. Jim is also an experienced player."