Learn German: Zum Glück sind wir das Jammern endlich los. - Fortunately, we are finally rid of the whining.

You are right that sein usually links two nominative nouns. However, the accusative here is triggered by the adjective los, not the verb. A small group of adjectives—including los (rid of), gewohnt (used to), and wert (worth)—directly require an accusative object to complete their meaning.

I have seen the verb loswerden used for 'to get rid of'. Is los a separable prefix in this sentence?

No, in this sentence los is an adjective used with the verb sein. While the verb loswerden describes the active process of getting rid of something, the phrase etwas los sein describes the state of already being rid of it. It sits at the end of the clause just like a separated prefix would, but grammatically it is a predicative adjective.

Why is Jammern capitalized?

This is a nominalized verb. You can turn any German infinitive verb (here, jammern, meaning to whine or complain) into a neuter noun by capitalizing it and adding the article das. It is the exact equivalent of the English gerund form, translated here as 'the whining'.

Why does the time adverb endlich come after the object das Jammern?