The 21-year-old athlete finished third in the T35 100m event, to mirror her placing five years ago, and crossed the line in 14.18 seconds behind China's Xia Zhou and Australian Isis Holt.
Lyle, from Dunbar, has cerebral palsy and adds the medal to her silver and two bronze collected at the Rio games in 2016.
Her run was just 0.28 seconds off her own personal best over 100m and Lyle will also aim for 200m glory in Japan.
Scottish competitors have already contributed to lifting Team GB into second in the medal table with awards for Fin Graham, Aileen McGlynn and Toni Shaw among them.
In the pool, Stephen Clegg, brother of fellow decorated Paralympians Libby and James, also picked up a bronze in the men’s S12 100m backstroke earlier on Friday.