Neither side were at full strength but the Springboks proved far too strong in a 55-6 victory in Port Elizabeth.
The 24-year-old Harley, who appeared in 24 PRO12 games for the Warriors this season, started in the back-row for Vern Cotter's side.
And while they shipped eight tries in all, the flanker insisted there were plenty of positives to be taken despite the heavy reversal.
"We definitely played better than the scoreline suggests," he said.
"The Springboks were able to take full advantage when we didn't do some things to the best of our ability.
"We performed well in periods of the match, we kept our structure, we came off the line and we hit them.
"They were intense for the whole 80 minutes which is something we aspire to.
"We will learn lessons from this and we can't lose sight of the bigger picture - three wins out of four on the trip. Overall, we are on an upward trajectory."
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