Schooling started at Embekweni Primary School on Monday and teaching was in full swing yesterday after a three-month boycott by 17 teachers.
But two teachers at the centre of a row with parents have been given "cool-off" leave by the Eastern Cape Education Department.
Parents had earlier accused the deputy principal, Phumzile Mtatase, and a teacher, Thembile Mncotsho, of being troublemakers.
The two were forced to stay at home while their 15 colleagues returned to work.
The teachers boycotted classes after parents accused them of abusing children, not teaching and using school funds for their own benefit.
Principal Pakamile Tyindyi confirmed that the 15 teachers had arrived at about 10am on Monday.
Before lessons started the teachers received learner-teacher support material from the school management team.
The resumption of classes came in the wake of a threat by Cape MEC for education Johnny Makgato that he would declare the school dysfunctional and freeze the salaries of all the teachers, including those who did not join in the boycott.
The school governing body (SGB) accused the South African Democratic Teachers Union (Sadtu) of dirty tricks after they allegedly called police to the school to protect teachers from parents.
Sergeant LZ Gongota, from Inyibiba police station in NU14, Mdantsane, said in a signed statement: "This serves to confirm that I visited the school because of an allegation by Sadtu [that] members were chased away and told not to enter the school premises.
"On my arrival, everything was well . [there was] no toyi-toying as was alleged. The principal was busy with the SGB, and the teachers were busy teaching pupils," the statement says.
Regional Sadtu chairman Sihle Mnguni said he did not know of any union members who had called the police.