More than 30 ambassadors and other Biden administration nominees were also confirmed.
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"I'm humbled and appreciative of President Biden's confidence he has placed in me and grateful for the Senate's bipartisan support," Emanuel said in a tweet. "As Ambassador, I will work tirelessly to deepen our ties as our countries confront common challenges. While Chicago will always be home, Amy and I look forward to this next chapter in Japan."
Eight Republicans ended up voting with a majority of Democrats to confirm Emanuel in a vote of 48-21.
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Emanuel also served as White House Chief of Staff during the Obama administration.
President Joe Biden nominated Emanuel for the position back in August.
"Rahm Emanuel has a lifetime of public service preparing him for this role," said Illinois Senator Dick Durbin in a statement. "Japan is an important strategic partner in Asia, particularly in light of our continued challenges from China. I have no doubt Rahm will be a strong voice for America in Japan."