The 20-year-old netted five goals in South Africa but while David Villa, Wesley Sneijder and Diego Forlan also scored five times, Mueller's three assists saw him edge out the trio for the top scorer award.
"This is just incredible for a newcomer to the World Cup. If anyone had told me I'd end on eight scorer points, I'd have said they were kidding me," Mueller said.
"It's an honour of course, but at the end of the day, I'd rather have had the World Cup itself."
The Bayern Munich star also beat fellow nominees Giovani Dos Santos of Mexico and Ghana midfielder Andre Ayew as the best young player after helping his side finish third with some terrific performances.
"It's a huge honour to be part of a group including the likes of Pele, Franz Beckenbauer, Michael Owen and the most recent winner, Lukas Podolski.
"For me personally, it's terrific confirmation of the work I've put in over the last year. I'm delighted my great run has continued here, and I've really enjoyed it too. The honour will be with me for all time, and it's a wonderful memento too."