James' Covalent Love took aim at a recent Bieber release, and was posted by the youth online.
James was named the idol winner during the festival's formal closing event at the University of Otago College of Education auditorium in Dunedin last night.
Like Bieber, James was born in Canada, but he never expected his music to be so popular.
"I don't think I'm a very good singer, so I wasn't confident about the song, but I really enjoyed writing the lyrics and knew a fair bit about the science I was trying to sing about," he said.
The John McGlashan College pupil figured Bieber's song about a boy wanting a girl fitted in well with his atom analogy.
"I knew a Justin Bieber parody would be great, and I wanted a popular song that was new," he said.
Judges said Covalent Love met all the criteria, including scientific content, lyrical ingenuity and performance suitability.
"What makes his song so cool is that it takes a traditional formula of a pop song and maintains that magic while exploring a critical chemical concept with depth, accuracy and pizzazz," judge Tom McFadden said.
"We've checked his submission for scientific accuracy and the final audio will be an expanded version of his original submission." Twenty-seven people from throughout New Zealand entered the competition, with the winning prize the chance to professionally record their entry at the University of Otago's Albany St studio and shoot a music video.
Dunedin's Tahuna Normal Intermediate School pupil Ella Cameron (13) won the competition's 8-14 age category, and Nelson-based American science teacher Justin Lee Tripp won the 22-plus age group.
