Manglin Pillay said that women preferred to "raise children than to be at the beck and call of shareholders".
He later apologized but Saice said it had terminated his contract due concern from its members.
Just 5% of Saice's 6,000 professional members are women.
South Africa's Commission for Gender Equality welcomed Mr Pillay's departure saying it would help the "fight against sexism and objectifying of women".
Gender Commission welcomes the termination of the South African Institution of Civil Engineering CEO Manglin Pillay's contract. This is a welcome move in fight against sexism and objectifying of women
He was discussing research on why fewer women take up careers in science, technology, engineering, and mathematics (STEM).
He wrote that "more men occupy high-profile executive posts... because of appetite for work load and extreme performance requirements at that level".
They attract "type-A personalities who are disagreeable at times, and highly competitive - workaholics... with almost no family, social or hobby time.
"The reason why women do not occupy these positions is that women choose to rather have the flexibility to dedicate themselves to more important enterprises, like family and raising children, than to be at the beck and call of shareholders".
The comments were criticised in August by South Africa's Science Minister Mmamoloko Kubayi-Ngubane, who said that the problem was a lack of support for women and not their attitudes, news site Fin24 reported.
Mr Pillay was also accused of blaming women for the lack of representation in STEM professions.
In the wake of the criticism he issued an apology in August "for antagonising and offending so many people".
But this was not enough to settle the controversy and Saice's board then decided Mr Pillay had to go.
Saice President Errol Kerst said that the response had been so large that the "ramifications of the article" could not be ignored.
South African Hema Vallabh, who helped found WomEng, which aims to attract women into engineering, said that this was not about a man "losing his job, but about sending the message that no form of discrimination will be tolerated".
For many the case of ManglinPillay was forgotten after the hype. But to those who continued to advocate for change, today you won. And just to be clear, the victory is not about losing his job, but about sending the message that no form of discrimination will be tolerated.