The world champion had come up just short in a controversial opening loss but controlled proceedings on Sunday (AEST) after another scrappy start.
Indeed, at the end of a week dominated by Rassie Erasmus' criticism of the officiating, referee Ben O'Keeffe took centre stage in the second try-less first half of the series.
But a pair of incisive kicks from Handre Pollard and Faf de Klerk then teed up scores for Makazole Mapimpi and Lukhanyo Am to deal the Lions their first defeat in four Tests.
The nature of Am's try could be considered contentious, however, and it might be Warren Gatland's turn to take issue with an under-the-spotlight official whose early warnings scarcely checked a frantic encounter.
Penalties provided the best opportunities for points, with Pollard opening the scoring after three minutes and Dan Biggar twice responding with his boot.
Pollard pulled a second effort wide to the left and the Springboks were dealt a blow as Pieter-Steph du Toit departed with an apparent shoulder injury before tempers flared.
Duhan van der Merwe made for the sin bin when his attempted kick instead caught Cheslin Kolbe, who soon followed his opponent for tackling Conor Murray in the air. A subsequent melee went unpunished.
Pollard found his range again, only for Biggar to keep the Lions three points ahead at half-time – albeit after the tourists passed up an opening when Robbie Henshaw could not ground the ball beyond the try line.
The quality that had been missing was immediately evident in the second period, however, as Pollard's kick picked out Mapimpi to thunder over on the left.
Pollard missed the conversion, which would have allowed Biggar to kick the Lions back in front had his fourth penalty not bounced away off the post.
Gatland's men struggled to put the Springboks under any extended pressure and were instead forced back, with De Klerk picking out Am, who appeared to control the ball with his forearm, rather than his palm.
Pollard found the target this time and another kick made absolutely sure. As a one-sided second half concluded in Lions territory, there was time for him to add one more, too, finishing with 17 points.