Wanted to pay extension but paid estimate instead. How do I fix this?

You can't fix it.

If you missed the deadline for requesting an extension, you don't have an extension of time to file.

@debfost 

This is what the TAXAUDIT webpage says

Many payment issues can be resolved with a phone call from the taxpayer to the IRS on the general phone line (800-829-1040 for Individuals and 800-829-4933 for Businesses). Another option is for the taxpayer to call the IRS at the number noted on any correspondence received, noting the specific balance due. In most cases, the agent on the phone can adjust the information in the IRS system and move the amounts from the incorrect tax year to the correct tax year. Once this change is completed, the IRS retains the date received in the system, and penalties and interest calculations are adjusted accordingly. This action can often resolve the full balance noted in the IRS correspondence or substantially reduce any penalties or interest payments requested.

notice the word is "many" not "all" but it doesn't hurt to try. 

How did you pay it?  By check or online?  There seemed to be a problem with the IRS applying extension payments to estimates.  Call the IRS and sort it out.  It might not have been something you did.