Given the push to lower the tackle height and modern penchant to hand out cards, Farrell and England were very fortunate to not concede a penalty at the least.
That contentious decision only added to a tense finish.
Boks first five-eighth Handre Pollard, after his pack delivered another scrum penalty on halfway, shaved the upright with a kick which would have put the Boks two points in-front with less than five minutes to play.
The visitors hammered away, controlling possession for those closing stages but, under immense pressure, this time England's defence held firm.
Over 80,000 erupted, their reaction perhaps tinged with more than a slice of relief.
Elliot Daly's long-range penalty, which regained the lead 10 minutes into the second spell, seemed to settle England as they released the shackles somewhat.
Before that, England were outmuscled for long periods.
More and more as the match opened up, England played out the backdoor with second man plays to create breathing room from the Boks' rush defence, allowing them to successfully attack the edges.
Farrell, despite taking a heavy knock to his hip, stepped up his running game to challenge the line, and nailed one clutch penalty on a wide angle in the final 10 minutes.
Ben Te'o logged a couple of crunching hits after just 29 minutes this year. The crowd found their voice. England's bench made an impact. The Boks began to tire. All of a sudden, the tide turned, and ultimately the Boks could not regain control.
England should beat this Boks team. With this test falling outside the designated window, Boks coach Rassie Erasmus was stripped of his experienced European-based stars - Willie le Roux, Francois Louw, Franco Mostert, Vincent Koch and Faf de Klerk, who ludicrously watched from a corporate box.
That England, albeit missing 16 players through injury, struggled for the full 80 minutes says everything about the spirit of this Boks team, and just how much Jones' side must improve in the space of seven days.
Playing like this against the All Blacks will not nearly be good enough.
On the backfoot throughout the first half, England were only saved only by Malcolm Marx's poor lineout throwing. Twice with the Boks five metres out, once with England down to 14 men, Marx missed his jumpers by overthrowing and, thus, letting England off the hook.
While so destructive elsewhere, this continues to be a costly deficiency in his game.
With England missing the physical presence of the Vunipola brothers, Billy and Mako, and down to their fourth-choice loose head prop and No 8 due to a raft of injuries, their heavily weakened pack were given an early lesson.
Maro Itoje's ill-discipline didn't help either; the lock sent to the bin for cynically killing the ball on his line, his third successive offence which saw Gardner rightly lose patience.
By this stage the Boks rolling maul was rumbling. England had no answers here, pinged at least four times for pushing before the jumper hit the ground or coming in the side.
The Boks dominated the scrums, too, even pulling off one tighthead, though England did get one back late to set up Farrell's winning kick.
Despite maintaining the upper hand in the first half, the anguish on Erasmus' face told the story. His men kept squandering opportunities, with loose carries another issue.
Boks midfielder Damian de Allende was a constant threat, hitting sharp angles, using deceptive footwork at the line and leg drive to offer consistent go forward.
Finally, after some nice short-side quick hands, Boks wing Sbu Nkosi finished the only try of the match to give the visitors something to show for their near complete control.
Their 8-6 half time advantage in no way reflected the state of affairs, with England falling off tackles and barely venturing into South Africa's 22, certainly not getting close to collecting any points other than from Farrell's boot.
With the limited ball they did have, England seemed bereft of ideas of how to use it; either throwing headless, wild passes or attempting to box kick their way downfield.
Tactically, England improved immeasurably in the second half, and they will take pride from their defensive effort.
But with the All Blacks looming large, the manner of this victory is no cause for celebration.
Scorers:
England: Elliot Daly pen, Owen Farrell pen 3
South Africa: Sbu Nkosi try, Handre Pollard pen 2
HT: 6-8, FULLTIME 12-11
