Hokkaido and Oita were the only two governor races to pit candidates backed by Abe's camp against major opposition parties including the Democratic Party of Japan (DPJ), which was ousted by Abe's camp in 2012 after a troubled three-year reign.
The victories by Hokkaido Governor Harumi Takahashi and Oita Governor Katsusada Hirose halted a losing streak for Abe's bloc in local polls including defeat on Okinawa island, host to a controversial U.S. Marines air base, and in rural Saga.
Takahashi's main rival, Noriyuki Sato, had run with the backing of the DPJ and other opposition parties on a platform that included opposition to nuclear power.
Read MoreWhy Japan Inc doesn't believe in Abenomics
Surveys show a majority of Japanese remain wary of restarting reactors.
"Opinion polls show most people are not feeling the 'love' of Abenomics and the worry was this might translate into a political setback," said Jeffrey Kingston, director of Asian studies at Temple University's Japan campus.
"These elections had postponed Abe moving ahead on unpopular policies and now they've got the elections out of the way, he can move forward," Kingston said.
Elections in smaller municipalities will be held on April 26.
The government is expected to present bills to parliament next month to ease limits of the pacifist constitution on Japan's military, marking a drastic policy shift which many voters oppose.
Japan and the United States are hoping to reach a deal ahead of Abe's visit to Washington this month to add momentum to a 12-nation free trade pact, the Trans-Pacific Partnership (TPP). A loss in rural Hokkaido could have complicated those efforts.
Opposition parties had trouble fielding candidates in many of Sunday's races, but an opposition candidate won an election for mayor of Sapporo, capital of Hokkaido, exit polls showed.