Can I apply a payment to a journal entry?

No you can't apply a payment to a journal entry.  You could enter a customer/job name on the journal entry then assign the same name to the deposit and the accounts receivable balance will net to zero but the transactions will never go away because they won't recognize each other.

You should have created an invoice, then paid it through accounts receivable.

I have used a journal entry to post a payment for both a bill payment and an AR open Invoice.  They are slightly different so I need additional information.  Are you attempting to post a payment for an AR open invoice? Or a bill payment? And what is the reason for not posting this through the normal QB pathways?