Nakaayi, 24, timed her race to perfection moving onto the shoulder of leader Ajee Wilson of the United States on the bend before kicking for home down the stretch.
Nakaayi took gold in 1min 58.04sec, with the fast-finishing Raevyn Rogers of the United States taking silver in 1:58.18.
Wilson had to settle for bronze in 1:58.84.
The 800m at this year's championships took place with the glaring absence of South Africa's two-time Olympic champion Semenya.
Semenya is not competing in Doha following a controversial Swiss court ruling which found in favour of new regulations effectively barring female athletes with naturally high testosterone levels from competing in the 800m.