Horne lasted only 10 minutes after coming on for Ruaridh Jackson at fly-half before his knee buckled under him while back-row forward Ryan Wilson hurt his shoulder late in the first half of the 30-17 loss in Nelspruit.
It is not known how long the Glasgow Warriors duo will be absent for but they will play no further part in the tour and follow Pat MacArthur, Kelly Brown and Geoff Cross in leaving early. There is more positive news for interim head coach Scott Johnson with regards Jackson though, with his shoulder injury not appearing to be as bad as first feared and he is staying with the squad as they prepare for their final game of the Incoming Series tournament against Italy in Pretoria on Saturday.
Scottish Rugby's lead physiotherapist Paul McGinley said: "The three most significant injuries from yesterday involved Peter Horne, Ryan Wilson and Ruaridh Jackson.
"Peter's knee injury will rule him out for the rest of the tour and he will return home for further investigation and follow-up. Likewise for Ryan with his shoulder injury. As far as Ruaridh is concerned, he suffered a blow to his shoulder and he will remain with us for on-going treatment this week.
"As ever, with an international match of this magnitude, a number of other players have reported to us with knocks and bumps. Steve Lawrie (hooker) who was unable to be involved yesterday, is improving following the back pain he experienced last week."
Ahead of their final match, Scotland have shifted base again, this time to Johannesburg, with the players still feeling a mixture of pride and frustration that they were unable to sustain the good work of the first 50 minutes against South Africa long enough to get the win.
Having been largely written off in the run-up to the game, the general feeling is that they went some way to erasing memories of their no-show against Samoa where they lost 27-17, even if they ultimately fell short of a first Scotland Test win in South Africa.
Wing Tommy Seymour, who had an encouraging debut, said: "Unfortunately it did not come off for us, but we need to be right about some areas. We showed a lot of heart. Unfortunately we did not get the win but we showed a lot of character. We need to take a lot of lessons from some of the stuff we did."
Lock Tim Swinson, who also impressed in his first Scotland appearance, added: "We played in the first half the way that we have talked about playing all week. We even played a bit in the second half like that but there were lapses that cost us dear."