Scotland went into the game seeking to extend their run of victories in America, Canada and Argentina.
However, Vern Cotter's side were no match for the hosts, who ran in eight tries in a 55-6 victory.
Scotland's only points came from two Duncan Weir penalties.
Head coach Cotter was ready to accept a dose of reality that had hit home after wins in the first three games of the tour. This was a step up and he found out that it could not be done with so many youngsters.
"It illustrated a lot of the things we are going to have to go away and work on to become competitive before the Rugby World Cup," he said.
"Honestly, much as we hate losing, especially by a score like that, there are some very positive things to come out of it.
"Adam Ashe played his first game at 20, Grant Gilchrist has come in as captain and done exceptionally well. I think all the players have done well.
'If we take away what we gave South Africa and add more of what we tried to develop on the field, then we can improve.
"We have to keep doing the good things and take away the bad stuff we didn't do well. If we don't offer as many opportunities to the opposition as we did today then we can shift in the right direction.
Cotter added: "It was a brave effort, the guys never gave up, now it is a question of channelling energy and decision making in the right way."