The government has told parents at 167 public schools to make alternative arrangements for their children on Friday.
A further 152 schools will operate with a modified program, while the state's remaining 608 schools will open as normal.
The Australian Education Union said 80 per cent of its members voted in favour of the strike after the government's "insulting" three per cent pay rise offer.
"Every day, over 35,000 South Australian students are going without a consistent teacher. It is a crisis affecting schools and preschools right across our state," SA union president Andrew Gohl said.
As well as a larger pay rise, the union is demanding the government ease workplace pressures by cutting instructional time by 20 per cent.
Education minister Blair Boyer says the state budget can't afford the reduction, which would equate to a billion dollars extra per year on top of the wage claim.
"We have to find meaningful workload reduction that doesn't mean kids in South Australian classrooms get a poorer quality education," he said.
"You've got two options: you've got kids have less education, or you backfill those teachers.
"You've got to find the staff and you've got to pay them. That's where the cost comes from."
But Mr Boyer believes negotiations are on the right track after the union dropped its demand for a school support officer in every classroom.
"Today's meeting was positive, there's no doubt about that," he said on Wednesday.
"I thought we made more ground than we've made at a lot of meetings that we've had.
"It's not muskets at dawn or anything like that, we are talking to each other and negotiating in good faith."
Education department head Martin Westwell said the full list of schools impacted is available on the department's website.
He urged parents to check the status of their child's school before sending them off, although staff will be at closed schools to make sure any children unexpectedly dropped off are safe.
To add to Friday's disruption, trams will not run before the morning peak as drivers strike over a pay and conditions dispute of their own.
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