The powerful lower house voted for the 60-year-old Abe with 328 votes against 73 for acting opposition leader Katsuya Okada.
The vote was followed by an upper house poll that officially confirmed Abe's reappointment as premier.
Abe's incumbent cabinet resigned en masse Wednesday morning, following the ruling coalition's victory in December 14 polls billed as a referendum on the pro-business Abe's economic growth blitz, dubbed Abenomics.
He will announce his new cabinet Wednesday afternoon, which local media said would be largely unchanged, and include deputy premier and finance minister Taro Aso as well as foreign minister Fumio Kishida.