The 27-year-old from Nassau surged to the line in 48.36sec, with Maileidy Paulino of the Dominican Republic taking silver and Allyson Felix of the United States claiming bronze.
Felix's bronze medal makes her the most decorated female athlete in track and field history with 10 medals won across five Olympic campaigns.
The 35-year-old American star, competing in her last Olympics in Tokyo, held off a fierce challenge from Jamaica's Stephenie Ann McPherson to take bronze in 49.46sec.
McPherson collapsed to the ground and began screaming loudly following the defeat, before being helped off the track in a wheelchair.
Miller-Uibo had beaten Felix to gold with a headlong dive for the line in a dramatic final at the 2016 Rio Olympics.
But her margin of victory was more emphatic in the Japanese capital as she ran a perfect tactical race, taking the lead off the final bend and charging home several metres clear of the field.
Miller-Uibo's win came 24 hours after the Bahamas' Gardiner had won the men's 400m gold on Thursday.