I have to pay a $3 underpayment penalty, as my taxes owed was >$1000. I choose "pay it now", but only taxes owed was paid, not the penalty. How do I pay IRS this fee?

Turbotax notified me that I had an underpayment penalty of $3 because my taxes owed was greater than $1000.  I wanted to pay this penalty along with the taxes owed in one transaction and picked the "pay it now" option on Turbotax.  When funds were withdrawn from my checking account, only my taxes owed was withdrawn and not the $3 penalty.  How do I pay the IRS the $3 penalty fee?  I want to pay this fee online if possible.