My thai partner is in australia on a 6 month tourist visa we just found out she is 3 months pregnant. She is due to leave early september can we apply for a visa to stay and have the baby here and if so which visa?? Any help would be great.

First of all you need to check the existing tourist visa and see if it has a No Further Stay condition and if so next step to have her stay would be to head into an Immi office and see if you get any joy with applying for a waiver - Australian Immigration Fact Sheet 52b. Waiving Visa Condition 8503 - "No Further Stay"
Getting a waiver is apparently difficult but you'll never know without trying and perhaps it'd help if you had marriage plans.

If there is no No Further Stay condition or you have a waiver, your alternatives would then seem to be either attempting to get a visa extension/further visitor visa [ being prepared to foot all the medical bills ] or get married or if you are in Vic., Tassie or ACT have a look at the possibility of getting a relationship registration [ could also be soon NSW ] .

https://online.justice.vic.gov.au/CA256902000FE154/Lookup/BDMApplication_Forms/$file/DomesticRelationship_ApplyToRegister.pdf [ link not working! ] for Vic. and you need to check with the relevant Births, Deaths and Marriages registry.

Doing either of the latter, she could apply for a partner visa and a bridging visa would be granted if the application was still being considered when the tourist visa ended.
There is quite a bit of documentation/evidence required however other than just getting married or having a relationship registered if that is possible.
Have a good read of the relevant sections via http://www.immi.gov.au/migrants/family/visa-options.htm and the Booklet #1 you'll see referred to.
But of course, first things first.