The tourists were leading 13-6 in a hard-fought match when replacement Emerging Springboks wing Danwel Demas went over in the corner for a try.
Willem de Waal then kept his nerve to slot his kick from the right-hand touchline, ending the Lions' hopes of a 100% record in the non-Test matches and preventing them from regaining momentum after Saturday's 26-21 defeat in the first Test.
A sharply-taken try in the first half by Keith Earls had been the difference between the sides before the dramatic conclusion.
The home side might even have clinched the win, had it not been for fly-half Earl Rose missing kickable penalties either side of the interval.
Chances were at a premium at Newlands because of the heavy rain and sodden pitch and few of the Lions were able to stake a claim for inclusion in the second Test.
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