The 2018 world all-around silver medallist extended her lead from qualifying in Gunma's Takasaki Arena, scoring a total of 112.564 to win by almost two points from Hatakeda Hitomi (110.598).
Hiraiwa Yuna was third with 108.631 while two-time Olympian Teramoto Asuka, who looked a certainty for the squad before tearing an Achilles tendon last February, dropped from fourth overnight to sixth with a score of 107.162.
Murakami's win saw her take a big step towards making this year's Tokyo 2020 Olympic Games.
The women with the top three combined all-around scores from this event and next month's NHK Trophy will be picked for the team with the fourth place decided by the selectors based on results and their potential to contribute to the the team.
That fourth spot could go to Teramoto, 25, who has been a key member of the Japanese team since 2011.
For Murakami, world champion on the floor in 2017, hopes of competing for medals are high after a strong day.
Leading the field by over a point thanks to her qualification score of 56.266, the 24-year-old posted higher scores on each apparatus with the exception of the balance beam.
She scored 14.733 for the vault, 14.266 on the uneven bars, 12.933 on the beam, and 14.366 for her floor exercise.