The 23-year-old, who played 18 times in the PRO12 last term, was captaining Scotland for just the second time and learned about leading a side the hard way as the Springboks ran in eight tries.
But despite the one-sided nature of the scoreline, Gilchrist insists the experience gained by the young side will be invaluable.
"It was a tough game. We had a poor start and that is not what we wanted against South Africa," he said.
"We knew it would be tough but we started slowly and that did not help our cause. As the half went on we got better but it is disappointing.
"We prepared all week to go flying into them and did not go out there fearing anyone, we came out as a young squad aiming to prove ourselves.
"There were a lot of guys given an opportunity to do our best.
"Every time we pull on the jersey we aim to do it proud. We are bitterly disappointed with the result but there were aspects out there with the young squad that we can be proud of."
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