State Medical Education Minister Kondru Murali hailed the apex court's order.
The verdict provided relief to thousands of students who had appeared for the exam in May for admission to medical and dental colleges in the state.
The state authorities last month declared the results of Engineering, Agriculture and Medical Common Entrance Test (EAMCET).
As many as 88,778 students qualified for admission to medical and agriculture courses out of 99,983 students who appeared in the test.
However, the authorities were waiting for the court verdict before announcing the counselling schedule. The orders have now cleared the decks for admissions to medical colleges.
Thousands of students in the state had also appeared in NEET, which was also held in May. With the Supreme Court's verdict, they will now breathe easy.
The Supreme Court Dec 13 last year said that the MCI, Dental Council of India, as well as the states, universities and other institutions, will be entitled to conduct their respective examinations for MBBS, BDS and post-graduate courses but shall not declare their results until further orders. On May 13, the court lifted the bar on the declaration of results.
Andhra Pradesh has 6,550 medical seats including 1,050 seats added by the Medical Council of India (MCI) - for the academic year 2013 -14.
The state government had sought time till 2014 to join NEET, citing low level of preparedness.
The apex court order has also been welcomed by private medical colleges, who had challenged the MCI notification. They argued that NEET was in a violation of their constitutional rights.
The private colleges were also not prepared to give 15 percent of their seats to the national pool.
The Supreme Court Thursday held that it was beyond the powers of the MCI to make such an arrangement of common entrance test both for government and private institutions.
A three-judge bench by a 2-1 verdict held that the MCI notification was ultra vires of the constitution.