Will my estimated federal tax payment be returned with my refund? I filed an extension and paid estimated tax but upon completing my return I am actually due a refund.

Your refund is already inclusive of the tax you paid at the time you filed your extension, if you reported the payment on your tax return.

You have to file your return to get your refund. 

Thanks @MinhT1! Both my extension and return were filed through TurboTax and accepted by the IRS. Unfortunately I did not notice an option to report estimated tax paid when I was filing my return, nor did TurboTax prefill my estimated tax paid even though I filed the extension through TurboTax! Line 26 on 1040 is blank and I am due a refund on my federal return even without the estimated tax payment factored in. Do I need to file an amended return to make sure my refund includes the estimated tax that I effectively overpaid?

The IRS should catch that and add it in for you.  Wait and see what the IRS sends for your refund.  

@leo-nevar  I'm on the same boat. Did you get your overpayment back from IRS or did you ended up file an amendment? Thanks!