The result left both teams on 10 points, but Rassie Erasmus' Springbok side will bid for another full five points when they round off their Pool B campaign against whipping boys Canada in Kobe on Tuesday.
Italy, however, are left with a testing game against in-form defending champions New Zealand -- who first take on Namibia on Sunday -- in Toyota on October 12.
Kolbe's try double was the highlight for the Springboks but the evening ended uncomfortably for the speedster when he limped off late in the game after twisting his ankle in a tackle.
Things didn't start well for Italy as tighthead prop Simone Ferrari was subbed off after injuring his leg in the first scrum within two minutes.
Spurning a shot at goal, the Boks were quickly on the scoreboard thanks to the lightning feet of jinking Toulouse pocket-rocket Kolbe.
A floated miss-pass from Willie Le Roux found the diminutive winger in a dead end down his right touchline, but he somehow stepped inside Tommaso Benvenuti and darted around Matteo Minozzi to dot down in the corner for a fine try Handre Pollard converted.
Italy fly-half Tommaso Allan and Pollard traded penalties as Italy coach Conor O'Shea was dealt a further blow when his second tighthead, replacement Marco Riccioni, was subbed off injured with just 18 minutes on the clock.
It meant English referee Wayne Barnes had no option but to order non-contested scrums, during which neither side has the right to push, starving South Africa of one of their key attacking weapons.
The Springboks, however, could still call on their big men, the likes of lock pairing Eben Etzebeth and Lood de Jager, and No 8 Duane Vermeulen, to take charge of their formidable driving mauls off attacking line-outs.
A wayward pass by Kolbe saw Le Roux fumble what would certainly have been a try, but hooker Mbongeni Mbonambi was on hand to dive over after one such efficient drive off a line-out. Pollard converted to make it 17-3 at half-time.
Incredibly, Italy lost a third prop at the start of the second period, loosehead Andrea Lovotti sent off for a needless tip-tackle after the whistle on Vermeulen.
It was the third red card of the World Cup after American John Quill and Uruguay's Facundo Gattas were both dismissed for high tackles.
Pollard hit a second penalty as Italy struggled to cope with the Springboks' all-encompassing defensive line speed and power runners in midfield.
The floodgates opened after centre Damian de Allende sparked a slick offloading attack before Pollard crosskicked on the recycle, Kolbe picking up on the second bounce to cross for his brace.
The fly-half sliced that conversion, but made no mistake after centre Lukhanyo Am grabbed an opportunistic intercept try, Italy's Gloucester flanker Jake Polledri forcing an inside pass with no one home.
Left winger Makazole Mapimpi then gathered a chip to cross for a deserved try after a great individual game, Pollard converting.
With Italy under the cosh Kolbe defied his size to bundle Minozzi touchwards with such force the Italy fullback attempted to keep the ball alive.
Bok replacement RG Snyman was on hand to intercept for the simplest of tries before Malcolm Marx popped over for the final word from an line-out maul.
South Africa will now look forward to putting Canada to the sword to line up an October 20 quarter-final game in Tokyo against the winner of Pool A, where things are yet to be decided between Ireland, Scotland, Japan and Samoa.