Many of the 60,387 in the crowd were rooting for the Pacific Islanders with the Springboks likely to meet hosts France should they progress to the knockouts, but while Tonga put on a brave showing, South Africa fed off their errors and had too much guile and experience.
The Boks scored tries through Cobus Reinach, Canan Moodie, Jessie Kriel, Deon Fourie, Willie le Roux, Marco van Staden and Kwagga Smith, but put in an error-strewn display, in part forced by the physicality of the Tongans.
The latter crossed for three scores through barrelling captain Ben Tameifuna, Fine Inisi and Patrick Pellegrini, the first time in 17 World Cup games the Boks have conceded three tries.
South Africa's win took them top of the pool with 15 points and into a strong position to qualify for the last eight, but they are not confirmed yet and must wait for the outcome of the clash between Ireland and Scotland next Saturday.
The only way the Boks can fail to progress is if Scotland get five points from that game and Ireland one, leaving all three teams on 15 points and the top two sides decided by points difference from their four matches.
There was another positive for South Africa on the day they were captained by Siya Kolisi for the 50th time. Fly half Handre Pollard made a successful return in his first test in 13 months as he kicked all his conversions and lasted 50 minutes.
His replacement Manie Libbok also converted three from three to give the Boks a 100% kicking record, something that has been a much talked about issue in their game.
Tonga spent much of the first half in the South African half, but the Boks scored three tries and led 21-8 at the break.
Scrum half Reinach took a quick penalty and dived over as Tonga were caught napping, before centre Moodie and hooker Fourie crossed.
But Tonga hit back as Tameifuna, officially the heaviest player at the World Cup weighing in at 151 kilograms, barged over from close range.
Inisi raced in at the corner and Pellegrini profited from a poor piece of Bok defence in the second half, much to the delight of their French hosts.
But South Africa chipped away at the scoreboard and kept Tonga at arms-length with four more tries for a win that was comfortable on paper, but hard-fought on the pitch.
