IRS Direct Pay

Can you make Form 1041 tax return payment with IRS Direct Pay?

Nope.

What types of returns, notices, or payment plans can I apply my Direct Pay payment to?
You can use Direct Pay to make payments on these payment types or towards the following returns:
•1040, 1040A, 1040EZ
•1040ES (Estimated tax)
•Installment Agreement
•1040X (Amended Return)
•4868 (Extension to file)
•5329 (Additional taxes on qualified plans)
•1040 Health Care payments (formerly called "Shared responsibility" payments)