The former Scottish first minister, now SNP MP, made the remark during a heated exchange in the Commons on Wednesday.
Mr Salmond had accused Ms Soubry of "demented" behaviour as she barracked him during the debate.
In a later tweet, she said his comments showed a "19th century attitude" to women, claiming he believed they should be "seen not heard".
The clash between the Conservative minister and former SNP leader came as MPs debated the upcoming appointments to Commons select committees.
Ms Soubry had suggested Mr Salmond should "move on" with his speech instead of detailing the Barnett formula, which determines regions' spending.
It prompted him to reply: "She should be setting an example to her new members, not cavorting about like some demented junior minister. Behave yourself, woman."
Responding to the exchange the following day, Ms Soubry tweeted: "Alex Salmond seems to think women should be seen not heard. His attitude belongs firmly in the 19th century.
"Salmond can dish it out but he can't take it!" she added.
It is not the first time the pair have clashed. Prior to the election they both appeared on the BBC's Andrew Marr Show, when Ms Soubry claimed the possibility of the senior SNP MP playing a role in government was "absolutely terrifying".
She said Mr Salmond's plans filled her with "absolute horror".
An SNP spokeswoman said: "There is no place for sexism in the House of Commons - and this was not an example of it. This was a boisterous but good-natured exchange and the remark was not intended to cause any offence."
Alex Salmond has been rebuked by Small Business Minister Anna Soubry after he told her to "behave yourself, woman".