Referee Alain Rolland called on television match official Stuart Dickinson for a verdict. The delay was excruciating for both teams and the 80,000 crowd packed into the Stade de France.
After numerous replays and a lengthy delay, Dickinson felt Cueto's trailing leg had clipped the touchline just before he planted the ball across the line and the try was disallowed.
The final was decided on penalties, 15-6 in the Springboks favour as Percy Montgomery and Frans Steyn outduelled Jonny Wilkinson.
Much like the 2011 decider, it was an unexpectedly tense conclusion after the team's blowout in pool play.
The Springboks were a well-drilled but cautious side under the coaching of Jake White and the captaincy of John Smit and picked up their second crown in four attempts against a committed England side which lacked much spark.
They had four men from their 2003 triumph-Wilkinson, Phil Vickery, Ben Kay and Jason Robinson while the Springboks had prop Os du Randt who was part of their successful 1995 campaign on home soil.