The top officials resigned after holding their final Cabinet meeting early Wednesday morning, officials at the prime minister's office said.
The resignations were a formality so that parliament's lower house, now controlled by Hatoyama's party following their landslide election victory last month, can vote him in as Japan's prime minister. Hatoyama's victory ends more than 50 years of nearly unbroken rule by Aso's Liberal Democratic Party.
Hatoyama, head of the left-of-center Democratic Party of Japan, has promised to shake up Japan's political system, cutting government waste, reinvigorating the world's second-largest economy and focusing policies on consumers, not big business.
Parliament was to convene in a special session later in the day to formally select the new prime minister. Hatoyama's party controls 308 of the 480 seats in the body's lower chamber, which selects the prime minister, virtually assuring him of the post.
"I am excited by the prospect of changing history," Hatoyama said early Wednesday.
He will have a tough job ahead.
His first task would be to name a Cabinet. Media reports said he had already chosen Katsuya Okada as his foreign minister and Hirohisa Fujii as his finance minister. Though Okada has never held a Cabinet post, Fujii was finance minister under a coalition government in 1993-94, the only time in its 55-year history that the Liberal Democrats had previously been ousted from power.
Hatoyama has a limited pool of seasoned politicians to choose from. His party, created a decade ago, has never held power, and nearly half of the Democrats' members of the lower house will be serving in their first terms in parliament.