Yes, the example is structurally (or syntactically) ambiguous. It could be parsed as (these are only partial):
(1) B [learned [that A telephoned after I visited]] (A telephoned afterwards)
(2) B [[learned that A telephoned] [after I visited]] (B learned afterwards)
The thing to notice is how soon after I visited branches off on its own. In (2), it separates at the second level of nesting that I have shown; in (1) it hasn't separated yet at the second level.
If you want to know more about this specific kind of structure, look up adjunct attachment. In fact, seaching for that turned up a paper Prosodic boundaries in adjunct attachment, which you might find especially interesting.
I think that prosody will not be of decisive help here because emphasizing or pausing could have other meanings, such as suggesting contrast, e.g., that something happened after rather than before. No pause anywhere helps disambiguate for me. In particular, I think that a pause between Albert and telephoned is mysterious and accomplishes nothing. Of course, that paper might have evidence to the contrary; I only glanced at the abstract.
In writing, I would move something to make the structure clearer.
After Isaiah visited, Betty learned that Albert telephoned.
This strongly suggests that after modifies learned.
Betty learned that, after Isaiah visited, Albert telephoned.
This strongly suggests that after modifies telephoned. I'm not confident that commas would help you enough because people are not consistent enough with their use, and they aren't I think helpful for this kind of thing even ideally.
If you want to know why moving helps, you can read about constituency tests here. I didn't see a good, focused intro to movement, but you can google more appropriately after you read about constituents. That is rather preliminary anyway.
And last but not least, I think that in most natural discourse, context actually serves to disambiguate the meanings. Context generally does a lot of work but often gets forgotten when one stops to think about something out of context.