The 1040NR Instructions say
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Pay Online
The IRS offers an electronic payment option that is right for you. Paying online is convenient and secure and helps make sure we get your payments on time. To pay your taxes online or for more information, go to irs.gov/payments. You can pay using any of the following methods.
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IRS Direct Pay. For online transfers directly from your checking or savings account at a U.S. bank or other financial institution in the United States at no cost to you, go to irs.gov/payments.
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Pay by Card. To pay by debit or credit card, go to irs.gov/payments. A convenience fee is charged by these service providers.
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Electronic Funds Withdrawal (EFW) is an integrated e-file/e-pay option offered when filing your federal taxes electronically using tax preparation software, through a tax professional, or the IRS at irs.gov/EFW.
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Online Payment Agreement. If you cannot pay in full by the due date of your tax return, you can apply for an online monthly installment agreement at irs.gov/OPA. Once you complete the online process, you will receive immediate notification of whether your agreement has been approved. A user fee is charged unless you are a low-income taxpayer meeting certain criteria.
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IRS2Go is the mobile application of the IRS; you can access Direct Pay or Pay by Card by downloading the application.
" All I can say is that it should work, according to the IRS' own instructions.
After the text above at the link, there are some additional paragraphs of explanation - you might try reading them as well to see if something pops.
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