Jasmine Jones of the US finished like a train to take silver in a personal best of 52.08, while Emma Zapletalova got a surprise bronze in a Slovakian national record of 53.00.
Bol won eight races in a row through the season and started her Tokyo trip by anchoring the Netherlands to silver in the mixed 4x400m relay.
In the absence of Olympic champion and world record-holder Sydney McLaughlin-Levrone, who won the 400 flat on Thursday, Bol was red-hot favourite on Friday and duly delivered.