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The university has also made the decision to no longer hold graduation ceremonies in Invercargill and graduates from Southland are to participate in Dunedin graduation ceremonies from next year.
Humanities pro-vice-chancellor Prof Brian Moloughney said both decisions were made primarily due to "financial considerations".
Running the campus' secondary education programme, in which 10 students had enrolled this year, required a "considerable cross-subsidisation from other areas of the college", Prof Moloughney said.
The programme will no longer be taught at the College of Education's Southland campus from next year.
He said dropping the programme would not affect "permanent staffing levels" at the Southland campus.
The decision comes before a post-merger review next month of the entire College of Education.
Prof Moloughney said the review would inform the "future directions" of the college.
There was no indication that further "significant changes" at the Southland campus were needed, he said.
A total of 195 students are enrolled in the university's Southland campus.
Otago University merged with the Dunedin College of Education in 2007.