Health issues prevented the women, who were in their 80s, from climbing out, officials said. They became unresponsive after overheating and developing hyperthermia.
The conflict that has put rebels in control of much of the east of the country has left victims with no legal recourse and dismantled many of the clinics that offered care.
Lawmakers allocated $6 billion this fiscal year for PEPFAR, the H.I.V. prevention and treatment program, but the administration has indicated it will release less than half of that.
The court's order was fractured, with the justices splitting over whether individual cancellations and the policy behind them could be challenged in a federal trial court.