The scrum-half came on as a second-half replacement for Mike Blair and the Glasgow man provided a much-needed spark to Scotland's play.
Winning only his second cap, Henry grabbed his try after running through a gap in the lineout to take Kelly Brown's instant catch and pass.
The home team continued to press but a combination of poor decision-making, great South African defence and marginal calls from the officials meant the Scots couldn't add to their tally.