Flyhalf Boshoff had earlier landed six penalties for the visitors to keep his side in touch with the Cheetahs who had their best Super Rugby campaign last season.
Both tries on Saturday were scored by the home side, by wingers Raymond Rhule and Cornall Hendricks who was making his debut.
Cheetahs flyhalf Johan Goosen, back after a lengthy injury layoff, converted both scores and added a penalty before being replaced by Elgar Watts who added one more three-pointer.
Watts then put a simple penalty wide just before Boshoff produced his moment of magic at the end.
The Lions are back in the competition after being replaced last year by the Port Elizabeth-based Southern Kings.
(Reporting by Nick Said in Cape Town)
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