The policy was confirmed in an urgent review which found a double rapist being placed in a women's jail did not put female prisoners at risk of harm.
However, the SPS said it received "conflicting" details on Isla Bryson.
It also called for an urgent review of admission rules for some inmates.
The investigation was ordered by Justice Secretary Keith Brown in the wake of public outcry after Bryson was initially housed in segregation at Cornton Vale prison in Stirling.
Bryson - who will be sentenced later this month for raping two women while she known as a man called Adam Graham - was then moved to a male wing at HMP Edinburgh.
In an interview with BBC Scotland, Mr Brown initially said the rule applied only to transgender people convicted of violence against women.
But after an intervention from a member of his staff, the justice secretary clarified that all transgender prisoners will go into an assessment in a prison service facility which matches the gender of their birth.
He added: "That will very often be a process which is undertaken in a segregated environment, before an assessment is made as to where the person goes.
"And if it turns out the person has that history [of violence against women or girls] then of course they will not be going to, if they are a trans woman, to the female estate."
SPS chief executive Teresa Medhurst said in a letter to Mr Brown that was published alongside a summary of the Bryson case review that she had ordered an urgent review of all transgender women in Scottish prisons.
She said: "Until these reviews are complete, any transgender person currently in custody and who has any history of violence against women - including sexual offences - will not be relocated from the male to the female estate.
"In addition, any newly convicted or remanded transgender prisoner will initially be placed in an establishment commensurate with their birth gender."
Under guidance drawn up in 2014, the prison service says "accommodation provided must be the one that best suits the person in custody's needs and should reflect the gender in which the person in custody is currently living."
However an updated SPS policy from last month stated that no newly convicted or remanded transgender prisoner with a history of violence against women would be housed in female prison facilities.
The latest change means that transgender women will now automatically go to a male prison regardless of whether or not they have previous convictions of violence against women. They will then be assessed before a decision is taken on where to place them longer-term.
However, the review says that in "exceptional circumstances" a transgender person with a history of violence against women could potentially be relocated to or placed in a prison which does not match their gender at birth, with ministerial approval.
Justice secretary explains prison gender policy