However, the couple said they would not join as the school management "continued to humiliate" them.
Tariq Bhat and Sumaya Bashir, both residents of Tral town in Pulwama, were working in boys and girls wings of Muslim Educational Institute Pampore respectively for the past several years.
But their services were abruptly terminated by the school management on November 30, the day they got married.
The school administration said the duo was relieved from their services as they were in a "romantic relationship" before marriage.
"They were having romance and it is not good for the 2,000 students of the school and 200 staff members working there. This can adversely affect the students," chairman of the school, Bashir Masoodi had said.
However, the school was censured for the decision on social media and the State Human Rights Commission also took suo motu cognisance of the news reports about the issue.
Justice Bilal Nazki, the chairperson of the Commission took serious note of the reports and asked the Director, School Education, Kashmir, and the school principal to file a report before the commission by December 18.
Following the cognisance of the SHRC, the government today intervened in the matter after which the school reinstated the couple.
"I called both the parties (the school management and the teachers) to my office today and the matter has been resolved.
The school has withdrawn the order (of couple s sacking) and they have been reinstated," deputy commissioner, Pulwama, Ghulam Mohammad Dar told PTI.
Mr Dar said the school management has asked the couple to resume their duties forthwith.
The couple, however, said they would not resume their duties as the school management humiliated them.
"Once the meeting with the deputy commissioner (DC) was over, the school management once again humiliated me outside the DC's office. There is no change in their behaviour and they said same things as they were saying before," Mr Bhat said.
He said he was not sure how the school management would treat them if they return to the school.
"They humiliated us just outside the DC office. What will they do once we are back in the school? So, we have decided to not join the school," he said.
The couple also claimed they had an arranged marriage.
"Ours was an arranged marriage. We got engaged a few months ago and the entire school management knew about it as Sumaya hosted a party for the staff members soon after the engagement ceremony," Mr Bhat had said earlier.