The court said earlier the doctors would face action if they carried on with the strike which had crippled services at many state-run hospitals across India.
A doctor from the New Delhi-based All India Institute of Medical Sciences (AIIMS), who did not want to be named, said: "Respecting the court's order, doctors and interns have decided to call off the strike with immediate effect."
Medical students who led the campaign against the greater reservation of seats for lower castes in state-funded colleges, were also expected to return to classes from Thursday, NDTV television channel said.
The agitation, which turned violent in New Delhi and Mumbai when police caned doctors, began soon after the government's announcement's last month that it would more than double the number of seats blocked for lower castes in state-funded colleges.
Protesters and many ordinary people say the move would undermine education and unfairly disadvantage deserving candidates from the upper castes.
The Supreme Court has asked the central government to explain the rationale behind the policy, and invited protesters to make their case in court rather than in the streets or hospitals.
"We will not countenance any inconvenience to the general public," the court's two-judge bench said earlier in the day.
The court also directed the government to drop all punitive action taken so far against the strikers and said sacking orders, if any, would also stand revoked if the doctors returned to duty.