Sheila Mechan's contract was terminated after only three weeks in the job. She had been suspended 10 days ago.
A union spokesman described the decision as "regrettable", but necessary after the breakdown of 'crucial working relationships' between Ms Mechan and other officials.
Glasgow-born Ms Mechan, 55, had only taken up the post on April 7.
There was no information about her departure on the SSTA website, which has gone offline.
A union spokesman said: "We can confirm that Sheila Mechan's employment as general secretary of the association was terminated.
"This follows her formal suspension on April 19, less than two weeks after taking up her position on April 7.
"This decision is regrettable, but given the immediate breakdown of a significant number of crucial working relationships, the SSTA decided it was in the association's best interests to move quickly to resolve the situation."
Former acting general secretary Alan McKenzie will take over her role until a permanent successor is found.
Mc Mechan, who has no teaching experience, but had worked in trade unions.
The SSTA had at the time of her appointment described her personality as 'ebbulient' and said she was a natural leader with a good sense of humour.