Bowie dipped for the line ahead of Marie-Josée Ta Lou by one-one hundredth of a second, as defending champion Dafne Schippers took the bronze.
Olympic champion Elaine Thompson faded badly over the final meters, as the Jamaican finished outside the medals.
Ta Lou puts down marker
With the big money on a two-horse battle between defending World champion Schippers and reigning Olympic champion Thompson for the Gold, Ta Lou announced her own intentions for sprint glory.
Running with Schippers in the second of three semi-finals, the Ivorian recovered from a slow start off the blocks, before surging past the Dutch athlete to finish first in a time of 10.87.
Though a slower time than that of Thompson, just three-one-hundredths separated the two. Schippers however, seemed satisfied with her time, with a chance for revenge over her Jamaican opponent in the final.
Of other significant note, Santos recorded a time of 10.91, with the Brazilian breaking the South American record. But could Ta Lou or outsider Bowie upset the odds?
Bowie stuns field
As silence fell on the London Stadium, Thompson flew out of the blocks in customary style. Ta Lou responded and accelerated away from the gun, pursued by the field.
At the 50m mark, the previously unfancied Ivorian was sprinting away from the pack - as Thompson failed to respond - and looked like easing to victory.
Bowie, however, a silver medalist in Rio 2016, went to her legs. With her final strides, the American gritted her teeth for the line. Both lunged for the line and after Ta Lou initially appeared to the cross marginally ahead, Bowie came up as the winner on the stadium's scoreboard, to the ecstasy of the American athlete.
The Olympic Stadium had seen another sensational 100 meters run after Justin Gatlin's shock win in the men's event 24 hours earlier. This time, however, the celebrations of another American, seemed rather more suited to the occasion.