Murakami, playing for the Tokyo-based Yakult Swallows, hit his 56th home run of the season on Monday, pushing him alone into second place on the single-season list. It was the Swallows' last regular-season game.
The hit came in the seventh inning against the DeNA Bay Stars at the Swallows' Jingu Stadium.
Murakami passed Japan's career home run leader Sadaharu Oh, Tuffy Rhodes, and Alex Cabrera, who all hit 55 in a season.
Wladimir Balentien holds the Nippon Professional Baseball's record of 60 home runs in a season, which he set with the Swallows in 2013.
Oh hit 55 home runs for the Yomiuri Giants in 1964, Rhodes did it with the Kintetsu Buffaloes in 2001, and Cabrera matched it with the Seibu Lions in 2002.
Murakami had gone 13 games without a home run after hitting his 54th and 55th on Sept. 13.