The stop-work action allowed teachers to gather at rallies across the city, including outside the office of Premier Steven Marshall.
It comes after 15 months of enterprise bargaining, culminating in the state government last week initiating conciliation proceedings in the employment tribunal.
The government has remained steadfast on its pay rise offer of 2.35 per cent for teachers and 3.35 per cent for principals, but has indicated it may negotiate other conditions.
Australian Education Union SA branch president Howard Spreadbury said it was crucial teachers had a say in negotiations.
He said the decision to take industrial action in the form of rolling one-hour stoppages during the last three weeks of term three was made through a member ballot.
"After all, our working conditions have a direct impact on the learning environment and learning outcomes for our students," he said.
A total of 48 schools were closed for an hour on Thursday, while two closed on Wednesday and one on Tuesday.