The wing struck in both halves as the Springboks condemned Steve Borthwick's men to a fifth defeat in a row and third this month following last-gasp 24-22 and 42-37 losses at home to New Zealand and Australia.
South Africa led 19-17 at the break after an open first half featuring five tries, with Grant Williams, Pieter-Steph du Toit and Kolbe all crossing for the Springboks.
Ollie Sleightholme and Sam Underhill went over for England in their first meeting with South Africa since the Springboks' dramatic 16-15 World Cup semi-final win in France last year.
A penalty exchange between England's Marcus Smith and South Africa's Handre Pollard left the Springboks 22-20 ahead going into the final quarter before Kolbe struck again in the 63rd minute.
South Africa replacement Gerhard Steenekamp was yellow-carded five minutes later but the Springboks saw the game out against an ill-disciplined England.
'We're content'
Springboks supremo Rassie Erasmus, however, had mixed emotions after making 12 changes to the team that started last week's 32-15 win over Scotland.
"Does the score (against England) really reflect how the game went?," he asked.
"Overall I guess when you play at Twickenham when you say that you're not happy with the performance but you beat them (England) by nine points, that would be arrogant...It wasn't fantastic. But we are content."
Freddie Steward, meanwhile, lamented England's ill-discipline, with the recalled full-back telling the BBC: "You cannot fault the effort but we didn't have enough today and credit to South Africa, they shut the game out well.
"Our discipline cost us. We talked about keeping our penalty count down in the week. We gave too many away and it cost us."
Erasmus had warned the Springboks to beware a "desperate" England and the hosts proved his point with a try inside four minutes to the delight of an 81,910 crowd.
Smith dummied a drop-goal before sending in Sleightholme, fresh from two tries off the bench against Australia, in the wing's first Test start.
In-form fly-half Smith then made light of a tricky conversion.
South Africa, however, soon levelled at 7-7 when scrum-half Williams, exploiting England's suspect ruck defence, burst between prop Ellis Genge and lock George Martin before side-stepping Steward for a superb solo try, with Manie Libbok adding the extras.
Smith's penalty edged England ahead but South Africa had their second try in the 17th minute.
Eben Etzebeth charged down Jack van Poortvliet's box-kick, with Smith's ensuing clearance also charged down in turn by Du Toit before the flanker dived on the loose ball for a try.
The Springboks soon had another try when fly-half Libbok's pinpoint cross-kick found Kolbe, who then side-stepped Steward in typical style with Libbok adding the extras.
England, to their credit, cut the deficit to two points when Underhill powered over from a close-range ruck for a 27th-minute try converted by Smith.
Both sides had tries overturned following video reviews early in the second half, with Springboks wing Kurt-Lee Arendse denied by a forward pass and Henry Slade's effort for England cancelled ou after Maro Itoje's illegal neck roll in the build-up.
Smith, however, edged England a point ahead at 20-19 in the 51st minute with a simple penalty only for replacement stand-off Pollard to land a monster penalty from just inside half-way that bounced off the crossbar.
England spent much of the second half deep in South Africa territory yet it was the Springboks who went two scores in front.
Damian de Allende powered his way past Ben Earl and Slade before the ball was worked to Kolbe, also a try-scorer in South Africa's 2019 World Cup final win over England.
Pollard converted Kolbe's 18th try in 39 Tests and the Springboks had the cushion of a nine-point lead.
