Müller's five goals and three assists edged out Spain's David Villa, the Netherlands' Wesley Sneijder and Uruguay's Diego Forlan – all three of whom also had five goals but fewer assists, meaning Müller won on a tie-break.
The Bayern Munich player's effort was all the more remarkable as he played one fewer games than either Villa or Sneijder, both of whom took part in Sunday night's uninspired final.
Uruguay's Forlan claimed the “golden ball” as the tournament's best player.
Müller went into the tournament with just two caps for Germany. He is the second straight German to win the golden boot after Miroslav Klose won in 2006, and also the second straight to win best young player after Lukas Podolski, also in 2006.
Müller's superb performance has established him as one of Germany's hottest young prospects in a team brimming with youthful players, whose average age is less than 25 – the country's youngest World Cup squad since 1934.
Critically, back-to-back yellow cards in the knock-out stage and quarter-finals kept Müller out of the semi-final against eventual cup winners Spain, leaving fans to wonder whether Germany could have won the match with the young star on the field.
He is also the second Müller to win the top-scoring prize. Gerd Müller, known as “the nation's bomber” took the golden boot in 1970, though he is no relation to the younger star.
“Of course I'm particularly happy to have won the golden boot 40 years after Gerd Müller,” the young Müller said on the team's plane from South Africa back to Germany.