Tries from Saracens' winger Nathan Earle and Exeter Chiefs' back rower Joel Conlon and a mammoth penalty from full back Aaron Morris saw England lift the title for the second year in a row after a great campaign.
It was the second title for Ross Moriarty who was a stand out performer on the night, matching his opponents' physicality throughout.
South Africa opened the scoring through IRB Junior Player of the Year Handre Pollard, and shortly after, Burns leveled the scores with a penalty of his own.
The Springboks scored the first try of the evening shortly after and it was a mistake that England could've rued. Henry Taylor took a quick tap and as he looked to spread the ball, his pass was off target.
The South Africans were quickest to gather and Pollard dinked a kick through that centre Jesse Kriel grabbed and ran home for a try, which his captain improved.
England's lineout was a major worry throughout the first half, hooker Tom Woolstencroft was under a lot of pressure as South Africa continued to work territory and play off English mistakes.
England reacted well and forced the South Africans into mistakes of their own and before half time, they worked themselves into a lead.
First, Aaron Morris impressively landed a 55m penalty, and then Saracens' centre Nick Tompkins held off a handful of tacklers to go close, before Burns fed winger Earle for a simple finish and put the English into a one-point lead at the turnaround.
Ross Moriarty was working hard in the contact area to keep England going forward and the back rower was prominent throughout along with captain Maro Itoje and Chiefs' Joel Conlon.
It was Conlon who touched down shortly after for what proved to be the crucial score as the English flexed their muscle to drive a rolling maul close and over the line with the man from Sandy Park emerging as the scorer.
Burns converted and England held an eight-point lead. Shortly after, Burns missed a penalty and South Africa made the fly half pay as Kriel got on the end of a sweeping move to dive over.
That was the end of the scoring as South Africa continued to bang on the door in an attempt to take the lead. England defended bravely and worked field position and comfortably saw out the game as Burns fittingly boomed the ball off the pitch to secure successive Junior World Championships.
Huge congratulations from all at Gloucester Rugby go to all of the England Rugby Under 20s squad, especially Billy Burns, Ross Moriarty and new faces Callum Braley and Henry Purdy!
England U20 captains Maro Itoje and Callum Braley lift the JWC trophy after their 21-20 victory v SA https://t.co/tpgurQmPNk- England Rugby (@EnglandRugby) June 20, 2014
We did it! Massive effort from everyone involved! World Champions. Auckland has me now! pic.twitter.com/MEdln1vSYG- Billy Burns (@BillyBurns10) June 20, 2014