Athletics' governing body said "biology has to trump gender identity" after welcoming the decision to permit restrictions in testosterone levels of female runners.
Double Olympic champion Caster Semenya twice appealed against the new International Association of Athletics Federations rule that prevents her from running the 800m without medication.
A Swiss court suspended the ruling which has now been lifted, though Semenya said she will not defend her 800m world title this year.
The IAAF said competitors now have "parity and clarity" before the championships in Doha, which begin on 28 September.
The ruling, which took effect on 8 May 2019, means those with differences of sexual development (DSD) must either take testosterone-reducing medication in order to compete in track events from 400m to the mile or change to another distance.
"I am very disappointed to be kept from defending my hard-earned title," Semenya, 28, said.
"But this will not deter me from continuing my fight for the human rights of all of the female athletes concerned."
The Swiss Federal Supreme Court, in its summing up, explained why it lifted the suspension, referring to the Court of Arbitration of Sport's initial reasoning as to why it turned down Semenya's appeal.
"The Swiss Federal Supreme Court concludes, in a first summary examination, that Caster Semenya's appeal does not appear with high probability to be well founded," it said.
It added that there would not be "fair competition" if there were women competing with 46 XY DSD genetic make-up, which includes Semenya.
The court dismissed the South African's allegations that she has been discriminated against or that there was "an infringement of personality and human dignity".