Team Tokai crossed the finish line in Adelaide on Thursday afternoon to claim back-to-back victories in the event, last held in 2009.
They narrowly beat the Netherlands' Nuon Solar in the race from Darwin, which started on Sunday.
Organisers said it was one of the closest finishes in the contest's 11-race history since 1987, with less than 30 kilometres separating first and second place.
The Japanese crew had dedicated their race to the reconstruction of their tsunami-stricken nation and its energy future following the related nuclear power plant crisis.
The dramatic contest saw Team Solar Philippines sidelined with a battery explosion which caused its car to ignite.
Earlier in the week wildfires swept through central Australia, forcing the entire race to a halt.
The University of Michigan was on track to finish in third place, with Dutch Solar Team Twente and Japan's Ashiya University expected to round out the top five.
The cars were allowed to store a small amount of energy, but the majority of their power had to come from the sun and the vehicle's kinetic forces.