I thought that turbotax would deduct my state tax owed from my federal tax refund and make the payment to state. Is that not the case?

[xmasbaby0]

You misunderstood.

It is not possible to pay your state tax due from your federal refund, nor is it possible to pay a federal tax due from a state refund.  The federal and state treasuries are completely separate from each other.  You may have seen a TurboTax summary of your federal and state amounts that confused you into thinking one was “paying” the other.  It is not. The ONLY thing you can pay for from a federal refund is your TurboTax fees if you chose that option.  

 If you have federal tax due you can pay by mailing your payment with the 1040V voucher, (which has the address printed on it, having the payment taken out of a designated bank account, or you can pay directly on the IRS website. 

https://www.irs.gov/payments/direct-pay 

https://ttlc.intuit.com/community/tax-payments/help/how-can-i-pay-my-federal-taxes/00/26212

https://ttlc.intuit.com/community/tax-payments/help/how-do-i-pay-my-irs-tax-due-with-a-check-or-mone... 

You must pay your state tax due using the state’s preferred method of receiving payment.  For most states that will be by making a payment to the state’s own tax website, or by mailing a check or money order.

https://ttlc.intuit.com/questions/1900884-what-are-my-options-for-getting-my-state-refund-or-for-pay...

https://ttlc.intuit.com/questions/1901670-how-do-i-contact-my-state-department-of-revenue

[Bsch4477]

No. Each taxing authority is separate and paid separately. You determine how and when the separate payments are made.